Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

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Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

Wim S

Hi,

We are updating from Apollo 2.0.6 to 2.4.1.  
We are used to being able to update or create a new gene by dragging RNAseq reads to the user curated track.

This does not seem to be possible anymore in Apollo 2.4.1
The track type that we used in APollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", does not seem to render split reads / introns in 2.4.1

Another track type,  "type": "WebApollo/View/Track/WebApolloAlignments2" does seem to display split reads / introns. But with this tracktype, the reads are not draggable anymore.
Only a context menu is available, from which a gene can be created per split aligned read.
These new genes can then sometimes be merged together in the user created annotation track, I guess based on overlap, or being book ended. 

Is the the WebApollo/View/Track/WebApolloAlignments2 track type the recommended way to display Illumina (split aligned) RNAseq reads, for the purpose of showing introns and exons?  Isn't there a track type, that both displays introns/split aligned reads, and is draggable?

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track?
In the case where there is no already existing gene in the user created annotation track, this would mean creating and merging together genes for almost each intron of a gene (if there are no split reads covering multiple introns).

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Thank you for in the information.

Wim

See also the screenshots below:

"type": "WebApollo/View/Track/DraggableAlignments"

"type": "WebApollo/View/Track/WebApolloAlignments2


"type": "WebApollo/View/Track/WebApolloAlignments2, resulting in a gene per split read/intron

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;">DraggableAlignments_cl.png

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;">WebApolloAlignments2.png

<a imageanchor="1" href="about:invalid#zClosurez" style="clear: left; margin-bottom: 1em; float: left; margin-right: 1em;">gene_per_intron.png

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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

nathandunn
Hey Wim,

Sorry this isn’t working out of the box for your Illimuna Reads. It sounds like it should.  DraggableAlignments (what you want) should roughly approximate WebApolloAlignments2

Some suggestions:

1 - The current version is 2.5.0, which might fix this, but I can’t recall anything specific past 2.4.1 that would have, but please try that first.  If you see the same result with DraggableAlignments.
2 - If it doesn’t work, can you create a GitHub issue with the context you’ve shown here and show screen shots of the the two tracks and any sample data: https://github.com/GMOD/Apollo/issues/new

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 

That sounds like what you will need to do until I get it fixed, but a screenshot would be helpful here. 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Unfortunately, there is a bug that prevents selecting and dragging up multiple BAM reads at the moment (https://github.com/GMOD/Apollo/issues/2352).   If you provide screen shots and some sample BAM reads (feel free to email), hopefully I can get both of these issues fixed.

Cheers,

Nathan


On Jan 22, 2020, at 7:30 AM, Wim S <[hidden email]> wrote:


Hi, 

We are updating from Apollo 2.0.6 to 2.4.1.   
We are used to being able to update or create a new gene by dragging RNAseq reads to the user curated track. 

This does not seem to be possible anymore in Apollo 2.4.1 
The track type that we used in APollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", does not seem to render split reads / introns in 2.4.1 

Another track type,  "type": "WebApollo/View/Track/WebApolloAlignments2" does seem to display split reads / introns. But with this tracktype, the reads are not draggable anymore. 
Only a context menu is available, from which a gene can be created per split aligned read. 
These new genes can then sometimes be merged together in the user created annotation track, I guess based on overlap, or being book ended.  

Is the the WebApollo/View/Track/WebApolloAlignments2 track type the recommended way to display Illumina (split aligned) RNAseq reads, for the purpose of showing introns and exons?  Isn't there a track type, that both displays introns/split aligned reads, and is draggable?

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 
In the case where there is no already existing gene in the user created annotation track, this would mean creating and merging together genes for almost each intron of a gene (if there are no split reads covering multiple introns). 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Thank you for in the information. 

Wim

See also the screenshots below:

"type": "WebApollo/View/Track/DraggableAlignments"

"type": "WebApollo/View/Track/WebApolloAlignments2


"type": "WebApollo/View/Track/WebApolloAlignments2, resulting in a gene per split read/intron

<a imageanchor="1" href="about:invalid#zClosurez" style="margin: 0px 1em 1em 0px; padding: 0px; border: 0px none; text-decoration: none; color: rgb(102, 17, 204); cursor: text; clear: left; float: left;" class=""><DraggableAlignments_cl.png>

<a imageanchor="1" href="about:invalid#zClosurez" style="margin: 0px 1em 1em 0px; padding: 0px; border: 0px none; text-decoration: none; color: rgb(102, 17, 204); cursor: text; clear: left; float: left;" class=""><WebApolloAlignments2.png>
<a imageanchor="1" href="about:invalid#zClosurez" style="margin: 0px 1em 1em 0px; padding: 0px; border: 0px none; text-decoration: none; color: rgb(102, 17, 204); cursor: text; clear: left; float: left;" class=""><gene_per_intron.png>

<DraggableAlignments_cl.png><WebApolloAlignments2.png><gene_per_intron.png>

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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

Wim S
Hi Nathan,

Thank you for the information. This sound like we would need to update twice more, first to 2.5 and then to 2.6 Do you know when 2.6 is coming out? 
And is there information somewhere about how to  perform this update? Does updating require a wipe of the user created annotation track / the mysql database? Or can the existing database content be kept?

Thank you.

Wim


Op donderdag 23 januari 2020 00:49:28 UTC+1 schreef Nathan Dunn:
Hey Wim,

Sorry this isn’t working out of the box for your Illimuna Reads. It sounds like it should.  DraggableAlignments (what you want) should roughly approximate WebApolloAlignments2

Some suggestions:

1 - The current version is 2.5.0, which might fix this, but I can’t recall anything specific past 2.4.1 that would have, but please try that first.  If you see the same result with DraggableAlignments.
2 - If it doesn’t work, can you create a GitHub issue with the context you’ve shown here and show screen shots of the the two tracks and any sample data: <a href="https://github.com/GMOD/Apollo/issues/new" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2Fnew\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDXdcsKb5ghdxonhGVhI3S3DJ10A&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2Fnew\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDXdcsKb5ghdxonhGVhI3S3DJ10A&#39;;return true;">https://github.com/GMOD/Apollo/issues/new

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 

That sounds like what you will need to do until I get it fixed, but a screenshot would be helpful here. 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Unfortunately, there is a bug that prevents selecting and dragging up multiple BAM reads at the moment (<a href="https://github.com/GMOD/Apollo/issues/2352" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2352\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhlETPdBcMdywO36pq84OEeYXzAg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2352\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhlETPdBcMdywO36pq84OEeYXzAg&#39;;return true;">https://github.com/GMOD/Apollo/issues/2352).   If you provide screen shots and some sample BAM reads (feel free to email), hopefully I can get both of these issues fixed.

Cheers,

Nathan


On Jan 22, 2020, at 7:30 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="4nWzFV-zEwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:


Hi, 

We are updating from Apollo 2.0.6 to 2.4.1.   
We are used to being able to update or create a new gene by dragging RNAseq reads to the user curated track. 

This does not seem to be possible anymore in Apollo 2.4.1 
The track type that we used in APollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", does not seem to render split reads / introns in 2.4.1 

Another track type,  "type": "WebApollo/View/Track/WebApolloAlignments2" does seem to display split reads / introns. But with this tracktype, the reads are not draggable anymore. 
Only a context menu is available, from which a gene can be created per split aligned read. 
These new genes can then sometimes be merged together in the user created annotation track, I guess based on overlap, or being book ended.  

Is the the WebApollo/View/Track/WebApolloAlignments2 track type the recommended way to display Illumina (split aligned) RNAseq reads, for the purpose of showing introns and exons?  Isn't there a track type, that both displays introns/split aligned reads, and is draggable?

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 
In the case where there is no already existing gene in the user created annotation track, this would mean creating and merging together genes for almost each intron of a gene (if there are no split reads covering multiple introns). 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Thank you for in the information. 

Wim

See also the screenshots below:

"type": "WebApollo/View/Track/DraggableAlignments"

"type": "WebApollo/View/Track/WebApolloAlignments2


"type": "WebApollo/View/Track/WebApolloAlignments2, resulting in a gene per split read/intron

<gene_per_intron.png>

<DraggableAlignments_cl.png><WebApolloAlignments2.png><gene_per_intron.png>


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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

nathandunn


On Jan 23, 2020, at 1:05 AM, Wim S <[hidden email]> wrote:

Hi Nathan,

Thank you for the information. This sound like we would need to update twice more, first to 2.5 and then to 2.6 Do you know when 2.6 is coming out?  

I would probably just upgrade to development (which will become 2.6), because if I have to fix something it will be there.

And is there information somewhere about how to  perform this update?


Does updating require a wipe of the user created annotation track / the mysql database? Or can the existing database content be kept?

You won’t lose any data at all assuming you’ve been able to successfully stop and start your server without losing data.

I always advocate backing up your database, regardless.  

If you want to be absolutely sure, can you share your rough setup of Apollo?

Nathan


Thank you. 

Wim


Op donderdag 23 januari 2020 00:49:28 UTC+1 schreef Nathan Dunn:
Hey Wim,

Sorry this isn’t working out of the box for your Illimuna Reads. It sounds like it should.  DraggableAlignments (what you want) should roughly approximate WebApolloAlignments2

Some suggestions:

1 - The current version is 2.5.0, which might fix this, but I can’t recall anything specific past 2.4.1 that would have, but please try that first.  If you see the same result with DraggableAlignments.
2 - If it doesn’t work, can you create a GitHub issue with the context you’ve shown here and show screen shots of the the two tracks and any sample data: https://github.com/GMOD/Apollo/issues/new

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 

That sounds like what you will need to do until I get it fixed, but a screenshot would be helpful here. 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Unfortunately, there is a bug that prevents selecting and dragging up multiple BAM reads at the moment (https://github.com/GMOD/Apollo/issues/2352).   If you provide screen shots and some sample BAM reads (feel free to email), hopefully I can get both of these issues fixed.

Cheers,

Nathan


On Jan 22, 2020, at 7:30 AM, Wim S <wim...@gmail.com> wrote:


Hi, 

We are updating from Apollo 2.0.6 to 2.4.1.   
We are used to being able to update or create a new gene by dragging RNAseq reads to the user curated track. 

This does not seem to be possible anymore in Apollo 2.4.1 
The track type that we used in APollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", does not seem to render split reads / introns in 2.4.1 

Another track type,  "type": "WebApollo/View/Track/WebApolloAlignments2" does seem to display split reads / introns. But with this tracktype, the reads are not draggable anymore. 
Only a context menu is available, from which a gene can be created per split aligned read. 
These new genes can then sometimes be merged together in the user created annotation track, I guess based on overlap, or being book ended.  

Is the the WebApollo/View/Track/WebApolloAlignments2 track type the recommended way to display Illumina (split aligned) RNAseq reads, for the purpose of showing introns and exons?  Isn't there a track type, that both displays introns/split aligned reads, and is draggable?

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 
In the case where there is no already existing gene in the user created annotation track, this would mean creating and merging together genes for almost each intron of a gene (if there are no split reads covering multiple introns). 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Thank you for in the information. 

Wim

See also the screenshots below:

"type": "WebApollo/View/Track/DraggableAlignments"

"type": "WebApollo/View/Track/WebApolloAlignments2


"type": "WebApollo/View/Track/WebApolloAlignments2, resulting in a gene per split read/intron

<gene_per_intron.png>

<DraggableAlignments_cl.png><WebApolloAlignments2.png><gene_per_intron.png>




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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

Wim S
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema.

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same.
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns.

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in.

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue.

Thank you.

Wim


# In Python code
# Get the Apollo BAM RNAconfig
bam_config
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


   
def get_rna_track_config(self):

       
# Add the BAM track configuration
        track
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

       
return track


In the trackList.json file this becomes
{
           
"autocomplete": "all",
           
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
           
"compress": 0,
           
"key": "DA_1155_DA_1155_01",
           
"label": "DA_1155_DA_1155_01",
           
"metadata": {
               
"analysis_project": "DA_1155",
               
"biomaterial_uid": "UID_XXXX",
               
"cultivar_type": "Unknown (public source)",
               
"data_format": "BAM",
               
"data_type": "RNA-seq Illumina",
               
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
               
"doi": "N/A",
               
"label": "DA_1155_DA_1155_01",
               
"library_layout": "N/A",
               
"rnaseq_exp_condition": "Experimental condition XXXXX",
               
"sequencing_project": "DA_1155",
               
"species": "Species_X",
               
"tissue": "Tissue_X"
           
},
           
"storeClass": "JBrowse/Store/SeqFeature/BAM",
           
"style": {
               
"className": "image"
           
},
           
"type": "WebApollo/View/Track/DraggableAlignments",
           
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
       
},



In the Apollo website this becomes

{
 
"maxFeatureSizeForUnderlyingRefSeq": 250000,
 
"subfeatureDetailLevel": 2,
 
"maxFeatureScreenDensity": 1.5,
 
"maxHeight": 1000,
 
"style": {
   
"arrowheadClass": "arrowhead",
   
"className": "image",
   
"_defaultHistScale": 4,
   
"_defaultLabelScale": 50,
   
"_defaultDescriptionScale": 120,
   
"minSubfeatureWidth": 1,
   
"maxDescriptionLength": 70,
   
"showLabels": false,
   
"label": "name,id",
   
"description": "note, description",
   
"centerChildrenVertically": true,
   
"renderClassName": "gray-center-30pct annot-apollo",
   
"subfeatureClasses": {
     
"UTR": "webapollo-UTR",
     
"CDS": "webapollo-CDS",
     
"exon": "container-100pct",
     
"intron": null,
     
"wholeCDS": null,
     
"start_codon": null,
     
"stop_codon": null,
     
"match_part": "darkblue-80pct"
   
},
   
"showMismatches": true,
   
"showSubfeatures": false
 
},
 
"hooks": {},
 
"events": {},
 
"menuTemplate": [
   
{
     
"label": "View details",
     
"title": "{type} {name}",
     
"action": "contentDialog",
     
"iconClass": "dijitIconTask"
   
},
   
{
     
"iconClass": "dijitIconFilter"
   
}
 
],
 
"layoutPitchY": 4,
 
"hideDuplicateReads": true,
 
"hideQCFailingReads": true,
 
"hideSecondary": true,
 
"hideSuXXlementary": true,
 
"hideMissingMatepairs": false,
 
"hideImproperPairs": false,
 
"hideUnmaXXed": true,
 
"hideUnsplicedReads": false,
 
"hideForwardStrand": false,
 
"hideReverseStrand": false,
 
"metadata": {
   
"library_layout": "N/A",
   
"data_format": "BAM",
   
"sequencing_project": "DA_1155",
   
"description": "Name=XXXXXX, SRA=SRR_XXXXXX",
   
"tissue": "Leaf",
   
"label": "DA_1155_DA_1155_01",
   
"cultivar_type": "Unknown (public source)",
   
"biomaterial_uid": "UID_XXXXXX",
   
"rnaseq_exp_condition": "Experimental condition XXXXXX",
   
"species": "Species X",
   
"data_type": "RNA-seq Illumina",
   
"analysis_project": "DA_1155",
   
"doi": "N/A"
 
},
 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
 
"autocomplete": "all",
 
"compress": 0,
 
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam",
 
"label": "DA_1155_DA_1155_01",
 
"type": "WebApollo/View/Track/DraggableAlignments",
 
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
 
"key": "DA_1155_DA_1155_01",
 
"baseUrl": "https://our_server.net/apollo2/14125950572413351251016927727/jbrowse/data/",
 
"index": 171
}











Op donderdag 23 januari 2020 15:58:22 UTC+1 schreef Nathan Dunn:


On Jan 23, 2020, at 1:05 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Bzd8RPjkEwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

Hi Nathan,

Thank you for the information. This sound like we would need to update twice more, first to 2.5 and then to 2.6 Do you know when 2.6 is coming out?  

I would probably just upgrade to development (which will become 2.6), because if I have to fix something it will be there.

And is there information somewhere about how to  perform this update?

<a href="https://genomearchitect.readthedocs.io/en/latest/Migration.html#migration-from-2-0-x-to-2-0-y-on-production" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FMigration.html%23migration-from-2-0-x-to-2-0-y-on-production\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHNXeXooFlQBx44D5u8LVGBq-hPYQ&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FMigration.html%23migration-from-2-0-x-to-2-0-y-on-production\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHNXeXooFlQBx44D5u8LVGBq-hPYQ&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Migration.html#migration-from-2-0-x-to-2-0-y-on-production

Does updating require a wipe of the user created annotation track / the mysql database? Or can the existing database content be kept?

You won’t lose any data at all assuming you’ve been able to successfully stop and start your server without losing data.

I always advocate backing up your database, regardless.  

If you want to be absolutely sure, can you share your rough setup of Apollo?

Nathan


Thank you. 

Wim


Op donderdag 23 januari 2020 00:49:28 UTC+1 schreef Nathan Dunn:
Hey Wim,

Sorry this isn’t working out of the box for your Illimuna Reads. It sounds like it should.  DraggableAlignments (what you want) should roughly approximate WebApolloAlignments2

Some suggestions:

1 - The current version is 2.5.0, which might fix this, but I can’t recall anything specific past 2.4.1 that would have, but please try that first.  If you see the same result with DraggableAlignments.
2 - If it doesn’t work, can you create a GitHub issue with the context you’ve shown here and show screen shots of the the two tracks and any sample data: <a href="https://github.com/GMOD/Apollo/issues/new" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2Fnew\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDXdcsKb5ghdxonhGVhI3S3DJ10A&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2Fnew\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDXdcsKb5ghdxonhGVhI3S3DJ10A&#39;;return true;">https://github.com/GMOD/Apollo/issues/new

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 

That sounds like what you will need to do until I get it fixed, but a screenshot would be helpful here. 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Unfortunately, there is a bug that prevents selecting and dragging up multiple BAM reads at the moment (<a href="https://github.com/GMOD/Apollo/issues/2352" rel="nofollow" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2352\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhlETPdBcMdywO36pq84OEeYXzAg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FGMOD%2FApollo%2Fissues%2F2352\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhlETPdBcMdywO36pq84OEeYXzAg&#39;;return true;">https://github.com/GMOD/Apollo/issues/2352).   If you provide screen shots and some sample BAM reads (feel free to email), hopefully I can get both of these issues fixed.

Cheers,

Nathan


On Jan 22, 2020, at 7:30 AM, Wim S <wim...@<a href="http://gmail.com/" style="margin:0px;padding:0px;border:0px none;text-decoration:none;color:rgb(102,17,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://gmail.com/&#39;;return true;" onclick="this.href=&#39;http://gmail.com/&#39;;return true;">gmail.com> wrote:


Hi, 

We are updating from Apollo 2.0.6 to 2.4.1.   
We are used to being able to update or create a new gene by dragging RNAseq reads to the user curated track. 

This does not seem to be possible anymore in Apollo 2.4.1 
The track type that we used in APollo 2.0.6, "type": "WebApollo/View/Track/DraggableAlignments", does not seem to render split reads / introns in 2.4.1 

Another track type,  "type": "WebApollo/View/Track/WebApolloAlignments2" does seem to display split reads / introns. But with this tracktype, the reads are not draggable anymore. 
Only a context menu is available, from which a gene can be created per split aligned read. 
These new genes can then sometimes be merged together in the user created annotation track, I guess based on overlap, or being book ended.  

Is the the WebApollo/View/Track/WebApolloAlignments2 track type the recommended way to display Illumina (split aligned) RNAseq reads, for the purpose of showing introns and exons?  Isn't there a track type, that both displays introns/split aligned reads, and is draggable?

Is it then recommend to create a new gene per split aligned read? And then to merge these together, with an existing gene, in the user created annotations track? 
In the case where there is no already existing gene in the user created annotation track, this would mean creating and merging together genes for almost each intron of a gene (if there are no split reads covering multiple introns). 

Isn't there a way to select multiple split aligned reads at once, for creating a gene via a single context menu click?

Thank you for in the information. 

Wim

See also the screenshots below:

"type": "WebApollo/View/Track/DraggableAlignments"

"type": "WebApollo/View/Track/WebApolloAlignments2


"type": "WebApollo/View/Track/WebApolloAlignments2, resulting in a gene per split read/intron

<gene_per_intron.png>

<DraggableAlignments_cl.png><WebApolloAlignments2.png><gene_per_intron.png>





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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

Wim S
We set the minimal amount of track config that we found necessary in Apollo 2.4.1. For the rest we rely on the defaults set by Apollo in the track config.

There is difference in the track config attributes set by Apollo 2.41 and Apollo 2.5.0. For example for these 2 style attributes.

Apollo 2.4.1
"arrowheadClass": null,
"renderClassName": null,

Apollo 2.5.0
"arrowheadClass": "arrowhead",
 
"renderClassName": "gray-center-30pct annot-apollo",

Setting in Apollo 2.5.0 these values to "null" as in Apollo 2.4.1. Does not fix the issue. But breaks the display even more.


See here for the full track config style attributes generated by default in Apollo 2.4.1 . Maybe we need to set more/other track config / style attributes explicitly in Apollo 2.5.0 compared to 2.4.1?

 "style": {
   
"arrowheadClass": null,
   
"className": "image",
   
"_defaultHistScale": 4,
   
"_defaultLabelScale": 50,
   
"_defaultDescriptionScale": 120,
   
"minSubfeatureWidth": 1,
   
"maxDescriptionLength": 70,
   
"showLabels": false,
   
"label": "name,id",
   
"description": "note, description",
   
"centerChildrenVertically": false,
   
"renderClassName": null,
   
"subfeatureClasses": {
     
"UTR": "webapollo-UTR",
     
"CDS": "webapollo-CDS",
     
"exon": "container-100pct",
     
"intron": null,
     
"wholeCDS": null,
     
"start_codon": null,
     
"stop_codon": null,
     
"match_part": "darkblue-80pct",
     
"M": "cigarM",
     
"D": null,
     
"N": "cigarN",
     
"E": "cigarEQ",
     
"X": "cigarX",
     
"I": null
   
},






Op donderdag 30 januari 2020 15:22:28 UTC+1 schreef Wim S:
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema.

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same.
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns.

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in.

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue.

Thank you.

Wim


# In Python code
# Get the Apollo BAM RNAconfig
bam_config
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


   
def get_rna_track_config(self):

       
# Add the BAM track configuration
        track
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

       
return track


In the trackList.json file this becomes
{
           
"autocomplete": "all",
           
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
           
"compress": 0,
           
"key": "DA_1155_DA_1155_01",
           
"label": "DA_1155_DA_1155_01",
           
"metadata": {
               
"analysis_project": "DA_1155",
               
"biomaterial_uid": "UID_XXXX",
               
"cultivar_type": "Unknown (public source)",
               
"data_format": "BAM",
               
"data_type": "RNA-seq Illumina",
               
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
               
"doi": "N/A",
               
"label": "DA_1155_DA_1155_01",
               
"library_layout": "N/A",
               
"rnaseq_exp_condition": "Experimental condition XXXXX",
               
"sequencing_project": "DA_1155",
               
"species": "Species_X",
               
"tissue": "Tissue_X"
           
},
           
"storeClass": "JBrowse/Store/SeqFeature/BAM",
           
"style": {
               
"className": "image"
           
},
           
"type": "WebApollo/View/Track/DraggableAlignments",
           
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
       
},



In the Apollo website this becomes

{
 
"maxFeatureSizeForUnderlyingRefSeq": 250000,
 
"subfeatureDetailLevel": 2,
 
"maxFeatureScreenDensity": 1.5,
 
"maxHeight": 1000,
 
"style": {
   
"arrowheadClass": "arrowhead",
   
"className": "image",
   
"_defaultHistScale": 4,
   
"_defaultLabelScale": 50,
   
"_defaultDescriptionScale": 120,
   
"minSubfeatureWidth": 1,
   
"maxDescriptionLength": 70,
   
"showLabels": false,
   
"label": "name,id",
   
"description": "note, description",
   
"centerChildrenVertically": true,
   
"renderClassName": "gray-center-30pct annot-apollo",
   
"subfeatureClasses": {
     
"UTR": "webapollo-UTR",
     
"CDS": "webapollo-CDS",
     
"exon": "container-100pct",
     
"intron": null,
     
"wholeCDS": null,
     
"start_codon": null,
     
"stop_codon": null,
     
"match_part": "darkblue-80pct"
   
},
   
"showMismatches": true,
   
"showSubfeatures": false
 
},
 
"hooks": {},
 
"events": {},
 
"menuTemplate": [
   
{
     
"label": "View details",
     
"title": "{type} {name}",
     
"action": "contentDialog",
     
"iconClass": "dijitIconTask"
   
},
   
{
     
"iconClass": "dijitIconFilter"
   
}
 
],
 
"layoutPitchY": 4,
 
"hideDuplicateReads": true,
 
"hideQCFailingReads": true,
 
"hideSecondary": true,
 
"hideSuXXlementary": true,
 
"hideMissingMatepairs": false,
 
"hideImproperPairs": false,
 
"hideUnmaXXed": true,
 
"hideUnsplicedReads": false,
 
"hideForwardStrand"</span

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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

nathandunn

So, I think there are two different issues here (please clarify):

1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:

2 - BAM tracks are no longer styled appropriately.

I think using 2.5.0 should be fine. 

Our demo server is here is running 2.5: https://genomearchitect.readthedocs.io/en/latest/Demo.html

If you use this link, you can see that both of these are rendered appropriately:

<a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group11.18:616279..617029&amp;organism=3836&amp;tracks=Official Gene Set v3.2,Forager RNA-Seq reads" class="">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group11.18:616279..617029&organism=3836&tracks=Official%20Gene%20Set%20v3.2,Forager%20RNA-Seq%20reads


The first thing I would try would be to remove additional styling and custom CSS from your trackList.json file, but otherwise I think your configuration looks good.  

The second thing would be to remove the Apollo track from your trackList.json file as Apollo should automatically add this.

For forager bam read entry for the demo site looks like this (there is no entry for the Apollo track):

 {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "bam/forager_Amel4.5_accepted_hits.bam",
         "label" : "Forager RNA-Seq reads",
         "type" : "WebApollo/View/Track/DraggableAlignments",
         "subfeatures" : true,
         "category" : "RNA-Seq BAMs",
         "key" : "Forager RNA-Seq reads"
      },

And the resultant image looks like this:




Nathan



On Jan 30, 2020, at 7:04 AM, Wim S <[hidden email]> wrote:

We set the minimal amount of track config that we found necessary in Apollo 2.4.1. For the rest we rely on the defaults set by Apollo in the track config. 

There is difference in the track config attributes set by Apollo 2.41 and Apollo 2.5.0. For example for these 2 style attributes. 

Apollo 2.4.1 
"arrowheadClass": null,
"renderClassName": null,

Apollo 2.5.0
"arrowheadClass": "arrowhead",
 
"renderClassName": "gray-center-30pct annot-apollo",

Setting in Apollo 2.5.0 these values to "null" as in Apollo 2.4.1. Does not fix the issue. But breaks the display even more. 


See here for the full track config style attributes generated by default in Apollo 2.4.1 . Maybe we need to set more/other track config / style attributes explicitly in Apollo 2.5.0 compared to 2.4.1?

 "style": {
    
"arrowheadClass": null,
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": false,
    
"renderClassName": null,
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct",
      
"M": "cigarM",
      
"D": null,
      
"N": "cigarN",
      
"E": "cigarEQ",
      
"X": "cigarX",
      
"I": null
    
},






Op donderdag 30 januari 2020 15:22:28 UTC+1 schreef Wim S:
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema. 

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same. 
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns. 

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in. 

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue. 

Thank you. 

Wim


# In Python code 
# Get the Apollo BAM RNAconfig 
bam_config 
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


    
def get_rna_track_config(self):

        
# Add the BAM track configuration
        track 
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

        
return track


In the trackList.json file this becomes
{
            
"autocomplete": "all",
            
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
            
"compress": 0,
            
"key": "DA_1155_DA_1155_01",
            
"label": "DA_1155_DA_1155_01",
            
"metadata": {
                
"analysis_project": "DA_1155",
                
"biomaterial_uid": "UID_XXXX",
                
"cultivar_type": "Unknown (public source)",
                
"data_format": "BAM",
                
"data_type": "RNA-seq Illumina",
                
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
                
"doi": "N/A",
                
"label": "DA_1155_DA_1155_01",
                
"library_layout": "N/A",
                
"rnaseq_exp_condition": "Experimental condition XXXXX",
                
"sequencing_project": "DA_1155",
                
"species": "Species_X",
                
"tissue": "Tissue_X"
            
},
            
"storeClass": "JBrowse/Store/SeqFeature/BAM",
            
"style": {
                
"className": "image"
            
},
            
"type": "WebApollo/View/Track/DraggableAlignments",
            
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
        
},



In the Apollo website this becomes

{
  
"maxFeatureSizeForUnderlyingRefSeq": 250000,
  
"subfeatureDetailLevel": 2,
  
"maxFeatureScreenDensity": 1.5,
  
"maxHeight": 1000,
  
"style": {
    
"arrowheadClass": "arrowhead",
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": true,
    
"renderClassName": "gray-center-30pct annot-apollo",
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct"
    
},
    
"showMismatches": true,
    
"showSubfeatures": false
  
},
  
"hooks": {},
  
"events": {},
  
"menuTemplate": [
    
{
      
"label": "View details",
      
"title": "{type} {name}",
      
"action": "contentDialog",
      
"iconClass": "dijitIconTask"
    
},
    
{
      
"iconClass": "dijitIconFilter"
    
}
  
],
  
"layoutPitchY": 4,
  
"hideDuplicateReads": true,
  
"hideQCFailingReads": true,
  
"hideSecondary": true,
  
"hideSuXXlementary": true,
  
"hideMissingMatepairs": false,
  
"hideImproperPairs": false,
  
"hideUnmaXXed": true,
  
"hideUnsplicedReads": false,
  
"hideForwardStrand"</span



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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

Wim S
Hi Nathan,

Thank you for the information and the link to the demo server.

2 - BAM tracks are no longer styled appropriately.

I changed in our code that generated the trackList config this line:

"className": "image"},

To these 2 lines:

"className": "alignment"},
"subfeatures": "true",

This seems to have fixed the display of the RNAseq tracks. The reads now look as on the demo server, and thus the intros and exons are visible again.  It is strange that the old config did work in Apollo 2.0.6.


1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:
The second issue was more about how to efficiently modify or add a gene in/to the user created annotation track. We pre-load this track with an existing predicted gene model. And then we would like to update or add genes to this tracks.
Updating can be done via dragging and dropping single split aligned RNAseq reads.

Creating a new gene is difficult to do via dragging and dropping a lot of single reads, and then merging them.
But we also have assembled transcripts in a GTF file (created by StringTie). These also I think can be dragged and dropped to create a new gene/transcript in the user created tracks via a single user action.

I need to check with the end users that the functionality is now as expected.  The biggest issue was the display of the RNAseq alignments, this now is fixed.

Thank you again for the information.



Op donderdag 30 januari 2020 23:26:31 UTC+1 schreef Nathan Dunn:

So, I think there are two different issues here (please clarify):

1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:

2 - BAM tracks are no longer styled appropriately.

I think using 2.5.0 should be fine. 

Our demo server is here is running 2.5: <a href="https://genomearchitect.readthedocs.io/en/latest/Demo.html" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FDemo.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHm_MXAkBJSFnY49hyuDnPvFBwRGg&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Demo.html

If you use this link, you can see that both of these are rendered appropriately:

<a href="http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group11.18:616279..617029&amp;organism=3836&amp;tracks=Official+Gene+Set+v3.2,Forager+RNA-Seq+reads" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup11.18%3A616279..617029%26organism%3D3836%26tracks%3DOfficial%2BGene%2BSet%2Bv3.2%2CForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGOnCQTVnKVl_fnCs_CMgPhKtrV9w&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdemo.genomearchitect.org%2FApollo2%2Fannotator%2FloadLink%3Floc%3DGroup11.18%3A616279..617029%26organism%3D3836%26tracks%3DOfficial%2BGene%2BSet%2Bv3.2%2CForager%2BRNA-Seq%2Breads\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGOnCQTVnKVl_fnCs_CMgPhKtrV9w&#39;;return true;">http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group11.18:616279..617029&organism=3836&tracks=Official%20Gene%20Set%20v3.2,Forager%20RNA-Seq%20reads


The first thing I would try would be to remove additional styling and custom CSS from your trackList.json file, but otherwise I think your configuration looks good.  

The second thing would be to remove the Apollo track from your trackList.json file as Apollo should automatically add this.

For forager bam read entry for the demo site looks like this (there is no entry for the Apollo track):

 {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "bam/forager_Amel4.5_accepted_hits.bam",
         "label" : "Forager RNA-Seq reads",
         "type" : "WebApollo/View/Track/DraggableAlignments",
         "subfeatures" : true,
         "category" : "RNA-Seq BAMs",
         "key" : "Forager RNA-Seq reads"
      },

And the resultant image looks like this:




Nathan



On Jan 30, 2020, at 7:04 AM, Wim S <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="XtIhzfAfDwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">wim...@...> wrote:

We set the minimal amount of track config that we found necessary in Apollo 2.4.1. For the rest we rely on the defaults set by Apollo in the track config. 

There is difference in the track config attributes set by Apollo 2.41 and Apollo 2.5.0. For example for these 2 style attributes. 

Apollo 2.4.1 
"arrowheadClass": null,
"renderClassName": null,

Apollo 2.5.0
"arrowheadClass": "arrowhead",
 
"renderClassName": "gray-center-30pct annot-apollo",

Setting in Apollo 2.5.0 these values to "null" as in Apollo 2.4.1. Does not fix the issue. But breaks the display even more. 


See here for the full track config style attributes generated by default in Apollo 2.4.1 . Maybe we need to set more/other track config / style attributes explicitly in Apollo 2.5.0 compared to 2.4.1?

 "style": {
    
"arrowheadClass": null,
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": false,
    
"renderClassName": null,
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct",
      
"M": "cigarM",
      
"D": null,
      
"N": "cigarN",
      
"E": "cigarEQ",
      
"X": "cigarX",
      
"I": null
    
},






Op donderdag 30 januari 2020 15:22:28 UTC+1 schreef Wim S:
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema. 

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same. 
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns. 

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in. 

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue. 

Thank you. 

Wim


# In Python code 
# Get the Apollo BAM RNAconfig 
bam_config 
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


    
def get_rna_track_config(self):

        
# Add the BAM track configuration
        track 
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

        
return track


In the trackList.json file this becomes
{
            
"autocomplete": "all",
            
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
            
"compress": 0,
            
"key": "DA_1155_DA_1155_01",
            
"label": "DA_1155_DA_1155_01",
            
"metadata": {
                
"analysis_project": "DA_1155",
                
"biomaterial_uid": "UID_XXXX",
                
"cultivar_type": "Unknown (public source)",
                
"data_format": "BAM",
                
"data_type": "RNA-seq Illumina",
                
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
                
"doi": "N/A",
                
"label": "DA_1155_DA_1155_01",
                
"library_layout": "N/A",
                
"rnaseq_exp_condition": "Experimental condition XXXXX",
                
"sequencing_project": "DA_1155",
                
"species": "Species_X",
                
"tissue": "Tissue_X"
            
},
            
"storeClass": "JBrowse/Store/SeqFeature/BAM",
            
"style": {
                
"className": "image"
            
},
            
"type": "WebApollo/View/Track/DraggableAlignments",
            
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
        
},



In the Apollo website this becomes

{
  
"maxFeatureSizeForUnderlyingRefSeq": 250000,
  
"subfeatureDetailLevel": 2,
  
"maxFeatureScreenDensity": 1.5,
  
"maxHeight": 1000,
  
"style": {
    
"arrowheadClass": "arrowhead",
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": true,
    
"renderClassName": "gray-center-30pct annot-apollo",
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct"
    
},
    
"showMismatches": true,
    
"showSubfeatures": false
  
},
  
"hooks": {},
  
"events": {},
  
"menuTemplate": [
    
{
      
"label": "View details",
      
"title": "{type} {name}",
      
"action": "contentDialog",
      
"iconClass": "dijitIconTask"
    
},
    
{
      
"iconClass": "dijitIconFilter"
    
}
  
],
  
"layoutPitchY": 4,
  
"hideDuplicateReads": true,
  
"hideQCFailingReads": true,
  
"hideSecondary": true,
  
"hideSuXXlementary": true,
  
"hideMissingMatepairs": false,
  
"hideImproperPairs": false,
  
"hideUnmaXXed": true,
  
"hideUnsplicedReads": false,
  
"hideForwardStrand"</span




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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

nathandunn

Wim,

Glad that these are hopefully of fixes. Let us know if not. 

I’ll try to see if I can’t get around to https://github.com/GMOD/Apollo/issues/2352 this week to fix the alignment reads issue, to see if it can be resolved, as well.

Thanks,

Nathan


On Feb 3, 2020, at 6:35 AM, Wim S <[hidden email]> wrote:

Hi Nathan, 

Thank you for the information and the link to the demo server. 

2 - BAM tracks are no longer styled appropriately.

I changed in our code that generated the trackList config this line:

"className": "image"},

To these 2 lines:

"className": "alignment"},
"subfeatures": "true",

This seems to have fixed the display of the RNAseq tracks. The reads now look as on the demo server, and thus the intros and exons are visible again.  It is strange that the old config did work in Apollo 2.0.6. 


1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:
The second issue was more about how to efficiently modify or add a gene in/to the user created annotation track. We pre-load this track with an existing predicted gene model. And then we would like to update or add genes to this tracks. 
Updating can be done via dragging and dropping single split aligned RNAseq reads. 

Creating a new gene is difficult to do via dragging and dropping a lot of single reads, and then merging them. 
But we also have assembled transcripts in a GTF file (created by StringTie). These also I think can be dragged and dropped to create a new gene/transcript in the user created tracks via a single user action. 

I need to check with the end users that the functionality is now as expected.  The biggest issue was the display of the RNAseq alignments, this now is fixed. 

Thank you again for the information. 



Op donderdag 30 januari 2020 23:26:31 UTC+1 schreef Nathan Dunn:

So, I think there are two different issues here (please clarify):

1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:

2 - BAM tracks are no longer styled appropriately.

I think using 2.5.0 should be fine. 

Our demo server is here is running 2.5: https://genomearchitect.readthedocs.io/en/latest/Demo.html

If you use this link, you can see that both of these are rendered appropriately:



The first thing I would try would be to remove additional styling and custom CSS from your trackList.json file, but otherwise I think your configuration looks good.  

The second thing would be to remove the Apollo track from your trackList.json file as Apollo should automatically add this.

For forager bam read entry for the demo site looks like this (there is no entry for the Apollo track):

 {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "bam/forager_Amel4.5_accepted_hits.bam",
         "label" : "Forager RNA-Seq reads",
         "type" : "WebApollo/View/Track/DraggableAlignments",
         "subfeatures" : true,
         "category" : "RNA-Seq BAMs",
         "key" : "Forager RNA-Seq reads"
      },

And the resultant image looks like this:




Nathan



On Jan 30, 2020, at 7:04 AM, Wim S <wim...@gmail.com> wrote:

We set the minimal amount of track config that we found necessary in Apollo 2.4.1. For the rest we rely on the defaults set by Apollo in the track config. 

There is difference in the track config attributes set by Apollo 2.41 and Apollo 2.5.0. For example for these 2 style attributes. 

Apollo 2.4.1 
"arrowheadClass": null,
"renderClassName": null,

Apollo 2.5.0
"arrowheadClass": "arrowhead",
 
"renderClassName": "gray-center-30pct annot-apollo",

Setting in Apollo 2.5.0 these values to "null" as in Apollo 2.4.1. Does not fix the issue. But breaks the display even more. 


See here for the full track config style attributes generated by default in Apollo 2.4.1 . Maybe we need to set more/other track config / style attributes explicitly in Apollo 2.5.0 compared to 2.4.1?

 "style": {
    
"arrowheadClass": null,
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": false,
    
"renderClassName": null,
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct",
      
"M": "cigarM",
      
"D": null,
      
"N": "cigarN",
      
"E": "cigarEQ",
      
"X": "cigarX",
      
"I": null
    
},






Op donderdag 30 januari 2020 15:22:28 UTC+1 schreef Wim S:
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema. 

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same. 
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns. 

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in. 

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue. 

Thank you. 

Wim


# In Python code 
# Get the Apollo BAM RNAconfig 
bam_config 
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


    
def get_rna_track_config(self):

        
# Add the BAM track configuration
        track 
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

        
return track


In the trackList.json file this becomes
{
            
"autocomplete": "all",
            
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
            
"compress": 0,
            
"key": "DA_1155_DA_1155_01",
            
"label": "DA_1155_DA_1155_01",
            
"metadata": {
                
"analysis_project": "DA_1155",
                
"biomaterial_uid": "UID_XXXX",
                
"cultivar_type": "Unknown (public source)",
                
"data_format": "BAM",
                
"data_type": "RNA-seq Illumina",
                
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
                
"doi": "N/A",
                
"label": "DA_1155_DA_1155_01",
                
"library_layout": "N/A",
                
"rnaseq_exp_condition": "Experimental condition XXXXX",
                
"sequencing_project": "DA_1155",
                
"species": "Species_X",
                
"tissue": "Tissue_X"
            
},
            
"storeClass": "JBrowse/Store/SeqFeature/BAM",
            
"style": {
                
"className": "image"
            
},
            
"type": "WebApollo/View/Track/DraggableAlignments",
            
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
        
},



In the Apollo website this becomes

{
  
"maxFeatureSizeForUnderlyingRefSeq": 250000,
  
"subfeatureDetailLevel": 2,
  
"maxFeatureScreenDensity": 1.5,
  
"maxHeight": 1000,
  
"style": {
    
"arrowheadClass": "arrowhead",
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": true,
    
"renderClassName": "gray-center-30pct annot-apollo",
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct"
    
},
    
"showMismatches": true,
    
"showSubfeatures": false
  
},
  
"hooks": {},
  
"events": {},
  
"menuTemplate": [
    
{
      
"label": "View details",
      
"title": "{type} {name}",
      
"action": "contentDialog",
      
"iconClass": "dijitIconTask"
    
},
    
{
      
"iconClass": "dijitIconFilter"
    
}
  
],
  
"layoutPitchY": 4,
  
"hideDuplicateReads": true,
  
"hideQCFailingReads": true,
  
"hideSecondary": true,
  
"hideSuXXlementary": true,
  
"hideMissingMatepairs": false,
  
"hideImproperPairs": false,
  
"hideUnmaXXed": true,
  
"hideUnsplicedReads": false,
  
"hideForwardStrand"</span






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Re: Recommended way of displaying and using Illumina RNAseq BAM files for updating a gene model in Apollo 2.4.1

nathandunn

FYI  https://github.com/GMOD/Apollo/issues/2352 is now fixed on the development branch.  

You can click and drag multiple reads on the same strand to create a single transcript.  

Thanks for reporting that error. 

Nathan




On Feb 3, 2020, at 8:43 AM, Nathan Dunn <[hidden email]> wrote:


Wim,

Glad that these are hopefully of fixes. Let us know if not. 

I’ll try to see if I can’t get around to https://github.com/GMOD/Apollo/issues/2352 this week to fix the alignment reads issue, to see if it can be resolved, as well.

Thanks,

Nathan


On Feb 3, 2020, at 6:35 AM, Wim S <[hidden email]> wrote:

Hi Nathan, 

Thank you for the information and the link to the demo server. 

2 - BAM tracks are no longer styled appropriately.

I changed in our code that generated the trackList config this line:

"className": "image"},

To these 2 lines:

"className": "alignment"},
"subfeatures": "true",

This seems to have fixed the display of the RNAseq tracks. The reads now look as on the demo server, and thus the intros and exons are visible again.  It is strange that the old config did work in Apollo 2.0.6. 


1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:
The second issue was more about how to efficiently modify or add a gene in/to the user created annotation track. We pre-load this track with an existing predicted gene model. And then we would like to update or add genes to this tracks. 
Updating can be done via dragging and dropping single split aligned RNAseq reads. 

Creating a new gene is difficult to do via dragging and dropping a lot of single reads, and then merging them. 
But we also have assembled transcripts in a GTF file (created by StringTie). These also I think can be dragged and dropped to create a new gene/transcript in the user created tracks via a single user action. 

I need to check with the end users that the functionality is now as expected.  The biggest issue was the display of the RNAseq alignments, this now is fixed. 

Thank you again for the information. 



Op donderdag 30 januari 2020 23:26:31 UTC+1 schreef Nathan Dunn:

So, I think there are two different issues here (please clarify):

1 - The user created annotation tracks (the yellow tracks at the top) no longer appear appropriately:

2 - BAM tracks are no longer styled appropriately.

I think using 2.5.0 should be fine. 

Our demo server is here is running 2.5: https://genomearchitect.readthedocs.io/en/latest/Demo.html

If you use this link, you can see that both of these are rendered appropriately:



The first thing I would try would be to remove additional styling and custom CSS from your trackList.json file, but otherwise I think your configuration looks good.  

The second thing would be to remove the Apollo track from your trackList.json file as Apollo should automatically add this.

For forager bam read entry for the demo site looks like this (there is no entry for the Apollo track):

 {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "bam/forager_Amel4.5_accepted_hits.bam",
         "label" : "Forager RNA-Seq reads",
         "type" : "WebApollo/View/Track/DraggableAlignments",
         "subfeatures" : true,
         "category" : "RNA-Seq BAMs",
         "key" : "Forager RNA-Seq reads"
      },

And the resultant image looks like this:




Nathan



On Jan 30, 2020, at 7:04 AM, Wim S <wim...@gmail.com> wrote:

We set the minimal amount of track config that we found necessary in Apollo 2.4.1. For the rest we rely on the defaults set by Apollo in the track config. 

There is difference in the track config attributes set by Apollo 2.41 and Apollo 2.5.0. For example for these 2 style attributes. 

Apollo 2.4.1 
"arrowheadClass": null,
"renderClassName": null,

Apollo 2.5.0
"arrowheadClass": "arrowhead",
 
"renderClassName": "gray-center-30pct annot-apollo",

Setting in Apollo 2.5.0 these values to "null" as in Apollo 2.4.1. Does not fix the issue. But breaks the display even more. 


See here for the full track config style attributes generated by default in Apollo 2.4.1 . Maybe we need to set more/other track config / style attributes explicitly in Apollo 2.5.0 compared to 2.4.1?

 "style": {
    
"arrowheadClass": null,
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": false,
    
"renderClassName": null,
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct",
      
"M": "cigarM",
      
"D": null,
      
"N": "cigarN",
      
"E": "cigarEQ",
      
"X": "cigarX",
      
"I": null
    
},






Op donderdag 30 januari 2020 15:22:28 UTC+1 schreef Wim S:
Hi Nathan,

Thank you again for the information. We do backup daily our mysql server and have configured in the groovy file to only update the database schema. 

I performed an update to Apollo 2.5, which went as it should I think. Only the issue remains the same. 
The "WebApollo/View/Track/DraggableAlignments"  Illumina RNAseq  tracks are still the black bars without the introns. 

We populate the Apollo trackList.json file via a piece of Python code that queries our repository that manages all our RNAseq bam files.  See the below pieces of code and track configuration that is results in. 

Does this track configuration look good to you?  Is there anything that I could/should change in this track config to get the RNAseq  reads/alignments visualized with introns and that are draggable to the user created content track?

Or is there anything else that I can try? I can also try an update to the the current Apollo development version, to see if this resolves the issue. 

Thank you. 

Wim


# In Python code 
# Get the Apollo BAM RNAconfig 
bam_config 
= bam.get_rna_track_config()

# Add the new BAM track to the list of tracks in the config
self.tracks_config.append(bam_config)


    
def get_rna_track_config(self):

        
# Add the BAM track configuration
        track 
= {"autocomplete": "all",
                 
"label": self.track_metadata.label,
                 
"style": {"className": "image"},
                 
"key": self.track_metadata.label,
                 
"storeClass": "JBrowse/Store/SeqFeature/BAM",
                 
"urlTemplate": self.relative_bam_path,
                 
"baiUrlTemplate": self.relative_bai_path,
                 
"compress": 0,
                 
"metadata": self.track_metadata.__dict__,
                 
"type": "WebApollo/View/Track/DraggableAlignments"}

        
return track


In the trackList.json file this becomes
{
            
"autocomplete": "all",
            
"baiUrlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam.bai",
            
"compress": 0,
            
"key": "DA_1155_DA_1155_01",
            
"label": "DA_1155_DA_1155_01",
            
"metadata": {
                
"analysis_project": "DA_1155",
                
"biomaterial_uid": "UID_XXXX",
                
"cultivar_type": "Unknown (public source)",
                
"data_format": "BAM",
                
"data_type": "RNA-seq Illumina",
                
"description": "Name=XXXX rep1, SRA=SRR_XXXXXX",
                
"doi": "N/A",
                
"label": "DA_1155_DA_1155_01",
                
"library_layout": "N/A",
                
"rnaseq_exp_condition": "Experimental condition XXXXX",
                
"sequencing_project": "DA_1155",
                
"species": "Species_X",
                
"tissue": "Tissue_X"
            
},
            
"storeClass": "JBrowse/Store/SeqFeature/BAM",
            
"style": {
                
"className": "image"
            
},
            
"type": "WebApollo/View/Track/DraggableAlignments",
            
"urlTemplate": "FileRepository/XX/GENOTYPESET/DA_1155_DA_1155_01/DA_1155_01-ready.bam"
        
},



In the Apollo website this becomes

{
  
"maxFeatureSizeForUnderlyingRefSeq": 250000,
  
"subfeatureDetailLevel": 2,
  
"maxFeatureScreenDensity": 1.5,
  
"maxHeight": 1000,
  
"style": {
    
"arrowheadClass": "arrowhead",
    
"className": "image",
    
"_defaultHistScale": 4,
    
"_defaultLabelScale": 50,
    
"_defaultDescriptionScale": 120,
    
"minSubfeatureWidth": 1,
    
"maxDescriptionLength": 70,
    
"showLabels": false,
    
"label": "name,id",
    
"description": "note, description",
    
"centerChildrenVertically": true,
    
"renderClassName": "gray-center-30pct annot-apollo",
    
"subfeatureClasses": {
      
"UTR": "webapollo-UTR",
      
"CDS": "webapollo-CDS",
      
"exon": "container-100pct",
      
"intron": null,
      
"wholeCDS": null,
      
"start_codon": null,
      
"stop_codon": null,
      
"match_part": "darkblue-80pct"
    
},
    
"showMismatches": true,
    
"showSubfeatures": false
  
},
  
"hooks": {},
  
"events": {},
  
"menuTemplate": [
    
{
      
"label": "View details",
      
"title": "{type} {name}",
      
"action": "contentDialog",
      
"iconClass": "dijitIconTask"
    
},
    
{
      
"iconClass": "dijitIconFilter"
    
}
  
],
  
"layoutPitchY": 4,
  
"hideDuplicateReads": true,
  
"hideQCFailingReads": true,
  
"hideSecondary": true,
  
"hideSuXXlementary": true,
  
"hideMissingMatepairs": false,
  
"hideImproperPairs": false,
  
"hideUnmaXXed": true,
  
"hideUnsplicedReads": false,
  
"hideForwardStrand"</span







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