not seeing tracks / annotation file

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not seeing tracks / annotation file

Heleen
Hi,

I have apollo running now in production. The only problem I am encountering is that I don't see tracks and thus nothing in the left screen. I've used the scripts to add data and I can add organisms and see them in Ref Sequence and the pulldown menus. The gff data I am using is like this:

##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region NC_017625.1 1 4630707
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=536056
NC_017625.1    RefSeq    region    1    4630707    .    +    .    ID=id0;Dbxref=taxon:536056;Is_circular=true;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=DH1
NC_017625.1    RefSeq    gene    33    1436    .    +    .    ID=gene0;Name=EcDH1_0001;Dbxref=GeneID:12707848;gbkey=Gene;locus_tag=EcDH1_0001
NC_017625.1    RefSeq    CDS    33    1436    .    +    0    ID=cds0;Name=YP_006089991.1;Parent=gene0;Note=KEGG: ssn:SSON_3652 chromosomal replication initiation protein%7ETIGRFAM:

I've used
bin/flatfile-to-json.pl --gff pyu_file.gff --trackLabel AnnotationsGff --out /opt/apollo/data
To add the annotation.

I guess I am doing something wrong there, but I cannot seem to figure out what. I am assuming it's the --type and tried several options there, but nothing worked.

Thanks,
Heleen.





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Re: not seeing tracks / annotation file

nathandunn

Heleen,

What does your trackList.json file look like? 

What do you see in the Track Panel (A)?

Also, if you click on either B or C, it should toggle the native track panel (on the left on and off) if you have customizations you want to see there.  


Nathan

On Feb 8, 2017, at 8:18 AM, Heleen <[hidden email]> wrote:

Hi,

I have apollo running now in production. The only problem I am encountering is that I don't see tracks and thus nothing in the left screen. I've used the scripts to add data and I can add organisms and see them in Ref Sequence and the pulldown menus. The gff data I am using is like this:

##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region NC_017625.1 1 4630707
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=536056
NC_017625.1    RefSeq    region    1    4630707    .    +    .    ID=id0;Dbxref=taxon:536056;Is_circular=true;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=DH1
NC_017625.1    RefSeq    gene    33    1436    .    +    .    ID=gene0;Name=EcDH1_0001;Dbxref=GeneID:12707848;gbkey=Gene;locus_tag=EcDH1_0001
NC_017625.1    RefSeq    CDS    33    1436    .    +    0    ID=cds0;Name=YP_006089991.1;Parent=gene0;Note=KEGG: ssn:SSON_3652 chromosomal replication initiation protein%7ETIGRFAM:

I've used
bin/flatfile-to-json.pl --gff pyu_file.gff --trackLabel AnnotationsGff --out /opt/apollo/data
To add the annotation.

I guess I am doing something wrong there, but I cannot seem to figure out what. I am assuming it's the --type and tried several options there, but nothing worked.

Thanks,
Heleen.




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: not seeing tracks / annotation file

Heleen
Hi Nathan,

Thanks again for your prompt response. We are in different time zones, so mine are a lot slower! I don't get the JBrowse window on the left (it's blank) and there are no tracks in the Tracks tab (right window). The toggle has no effect. I can use JBrowse (volvox sample) from the subdirectory /jbrowse. TtrackList.json looks like this:
{
   "formatVersion" : 1,
   "tracks" : [
      {
         "type" : "SequenceTrack",
         "seqType" : "dna",
         "label" : "DNA",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "key" : "Reference sequence",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "category" : "Reference sequence",
         "chunkSize" : 20000
      },
      {
         "label" : "AnnotationsGff",
         "style" : {
            "className" : "feature"
         },
         "trackType" : null,
         "type" : "FeatureTrack",
         "key" : "AnnotationsGff",
         "urlTemplate" : "tracks/AnnotationsGff/{refseq}/trackData.json",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "compress" : 0
      }
   ]
}

I tried changing trackType to "Gene" but that did not work. I can export the sequence in the Ref Sequence Tab.


Inline afbeelding 2


Thanks!
Heleen.


2017-02-08 17:57 GMT+01:00 Nathan Dunn <[hidden email]>:

Heleen,

What does your trackList.json file look like? 

What do you see in the Track Panel (A)?

Also, if you click on either B or C, it should toggle the native track panel (on the left on and off) if you have customizations you want to see there.  


Nathan

On Feb 8, 2017, at 8:18 AM, Heleen <[hidden email]> wrote:

Hi,

I have apollo running now in production. The only problem I am encountering is that I don't see tracks and thus nothing in the left screen. I've used the scripts to add data and I can add organisms and see them in Ref Sequence and the pulldown menus. The gff data I am using is like this:

##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region NC_017625.1 1 4630707
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=536056
NC_017625.1    RefSeq    region    1    4630707    .    +    .    ID=id0;Dbxref=taxon:536056;Is_circular=true;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=DH1
NC_017625.1    RefSeq    gene    33    1436    .    +    .    ID=gene0;Name=EcDH1_0001;Dbxref=GeneID:12707848;gbkey=Gene;locus_tag=EcDH1_0001
NC_017625.1    RefSeq    CDS    33    1436    .    +    0    ID=cds0;Name=YP_006089991.1;Parent=gene0;Note=KEGG: ssn:SSON_3652 chromosomal replication initiation protein%7ETIGRFAM:

I've used
bin/flatfile-to-json.pl --gff pyu_file.gff --trackLabel AnnotationsGff --out /opt/apollo/data
To add the annotation.

I guess I am doing something wrong there, but I cannot seem to figure out what. I am assuming it's the --type and tried several options there, but nothing worked.

Thanks,
Heleen.




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: not seeing tracks / annotation file

nathandunn

If you are using the Volvox sample in JBrowse you should be seeing 2 reference sequences and you would just point to the existing directory that has “trackList.json” defined:

http://icebox.lbl.gov/Apollo2/annotator/loadLink?loc=ctgA:0..50001&organism=228544&tracks=ExampleFeatures 

[hidden email] / demo

In the demo, I’m point to: <path_to_jbrowse>/sample_data/json/volvox/)

The directory should look like this (tracks.conf and names are both optional):

names/            tracks/          
seq/              trackList.json    tracks.conf


So, it could be data error, or it could be installation problems.  What errors do you see in your javascript console on load?

Nathan

> On Feb 9, 2017, at 6:35 AM, Heleen <[hidden email]> wrote:
>
> Hi Nathan,
>
> Thanks again for your prompt response. We are in different time zones, so mine are a lot slower! I don't get the JBrowse window on the left (it's blank) and there are no tracks in the Tracks tab (right window). The toggle has no effect. I can use JBrowse (volvox sample) from the subdirectory /jbrowse. TtrackList.json looks like this:
> {
>    "formatVersion" : 1,
>    "tracks" : [
>       {
>          "type" : "SequenceTrack",
>          "seqType" : "dna",
>          "label" : "DNA",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
>          "key" : "Reference sequence",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "category" : "Reference sequence",
>          "chunkSize" : 20000
>       },
>       {
>          "label" : "AnnotationsGff",
>          "style" : {
>             "className" : "feature"
>          },
>          "trackType" : null,
>          "type" : "FeatureTrack",
>          "key" : "AnnotationsGff",
>          "urlTemplate" : "tracks/AnnotationsGff/{refseq}/trackData.json",
>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>          "compress" : 0
>       }
>    ]
> }
>
> I tried changing trackType to "Gene" but that did not work. I can export the sequence in the Ref Sequence Tab.
>
>
> <image.png>
>
>
> Thanks!
> Heleen.
>
>
> 2017-02-08 17:57 GMT+01:00 Nathan Dunn <[hidden email]>:
>
> Heleen,
>
> What does your trackList.json file look like?
>
> What do you see in the Track Panel (A)?
>
> Also, if you click on either B or C, it should toggle the native track panel (on the left on and off) if you have customizations you want to see there.  
>
> <Screen Shot 2017-02-08 at 8.56.20 AM.png>
>
> Nathan
>
>> On Feb 8, 2017, at 8:18 AM, Heleen <[hidden email]> wrote:
>>
>> Hi,
>>
>> I have apollo running now in production. The only problem I am encountering is that I don't see tracks and thus nothing in the left screen. I've used the scripts to add data and I can add organisms and see them in Ref Sequence and the pulldown menus. The gff data I am using is like this:
>>
>> ##gff-version 3
>> #!gff-spec-version 1.20
>> #!processor NCBI annotwriter
>> ##sequence-region NC_017625.1 1 4630707
>> ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=536056
>> NC_017625.1    RefSeq    region    1    4630707    .    +    .    ID=id0;Dbxref=taxon:536056;Is_circular=true;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=DH1
>> NC_017625.1    RefSeq    gene    33    1436    .    +    .    ID=gene0;Name=EcDH1_0001;Dbxref=GeneID:12707848;gbkey=Gene;locus_tag=EcDH1_0001
>> NC_017625.1    RefSeq    CDS    33    1436    .    +    0    ID=cds0;Name=YP_006089991.1;Parent=gene0;Note=KEGG: ssn:SSON_3652 chromosomal replication initiation protein%7ETIGRFAM:
>>
>> I've used
>> bin/flatfile-to-json.pl --gff pyu_file.gff --trackLabel AnnotationsGff --out /opt/apollo/data
>> To add the annotation.
>>
>> I guess I am doing something wrong there, but I cannot seem to figure out what. I am assuming it's the --type and tried several options there, but nothing worked.
>>
>> Thanks,
>> Heleen.
>>
>>
>>
>>
>> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
>> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: not seeing tracks / annotation file

Heleen
Hi Nathan,

There was a problem with the .gff3 file I think. Not sure what, it made the trackData.json file very large and of incorrect format.

I copied some sample folders and added an organism pointing to that folder and can see tracks for that organism.

Thanks!
Heleen.


2017-02-09 21:34 GMT+01:00 Nathan Dunn <[hidden email]>:

If you are using the Volvox sample in JBrowse you should be seeing 2 reference sequences and you would just point to the existing directory that has “trackList.json” defined:

http://icebox.lbl.gov/Apollo2/annotator/loadLink?loc=ctgA:0..50001&organism=228544&tracks=ExampleFeatures

[hidden email] / demo

In the demo, I’m point to: <path_to_jbrowse>/sample_data/json/volvox/)

The directory should look like this (tracks.conf and names are both optional):

names/            tracks/
seq/              trackList.json    tracks.conf


So, it could be data error, or it could be installation problems.  What errors do you see in your javascript console on load?

Nathan

> On Feb 9, 2017, at 6:35 AM, Heleen <[hidden email]> wrote:
>
> Hi Nathan,
>
> Thanks again for your prompt response. We are in different time zones, so mine are a lot slower! I don't get the JBrowse window on the left (it's blank) and there are no tracks in the Tracks tab (right window). The toggle has no effect. I can use JBrowse (volvox sample) from the subdirectory /jbrowse. TtrackList.json looks like this:
> {
>    "formatVersion" : 1,
>    "tracks" : [
>       {
>          "type" : "SequenceTrack",
>          "seqType" : "dna",
>          "label" : "DNA",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
>          "key" : "Reference sequence",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "category" : "Reference sequence",
>          "chunkSize" : 20000
>       },
>       {
>          "label" : "AnnotationsGff",
>          "style" : {
>             "className" : "feature"
>          },
>          "trackType" : null,
>          "type" : "FeatureTrack",
>          "key" : "AnnotationsGff",
>          "urlTemplate" : "tracks/AnnotationsGff/{refseq}/trackData.json",
>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>          "compress" : 0
>       }
>    ]
> }
>
> I tried changing trackType to "Gene" but that did not work. I can export the sequence in the Ref Sequence Tab.
>
>
> <image.png>
>
>
> Thanks!
> Heleen.
>
>
> 2017-02-08 17:57 GMT+01:00 Nathan Dunn <[hidden email]>:
>
> Heleen,
>
> What does your trackList.json file look like?
>
> What do you see in the Track Panel (A)?
>
> Also, if you click on either B or C, it should toggle the native track panel (on the left on and off) if you have customizations you want to see there.
>
> <Screen Shot 2017-02-08 at 8.56.20 AM.png>
>
> Nathan
>
>> On Feb 8, 2017, at 8:18 AM, Heleen <[hidden email]> wrote:
>>
>> Hi,
>>
>> I have apollo running now in production. The only problem I am encountering is that I don't see tracks and thus nothing in the left screen. I've used the scripts to add data and I can add organisms and see them in Ref Sequence and the pulldown menus. The gff data I am using is like this:
>>
>> ##gff-version 3
>> #!gff-spec-version 1.20
>> #!processor NCBI annotwriter
>> ##sequence-region NC_017625.1 1 4630707
>> ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=536056
>> NC_017625.1    RefSeq    region    1    4630707    .    +    .    ID=id0;Dbxref=taxon:536056;Is_circular=true;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=DH1
>> NC_017625.1    RefSeq    gene    33    1436    .    +    .    ID=gene0;Name=EcDH1_0001;Dbxref=GeneID:12707848;gbkey=Gene;locus_tag=EcDH1_0001
>> NC_017625.1    RefSeq    CDS    33    1436    .    +    0    ID=cds0;Name=YP_006089991.1;Parent=gene0;Note=KEGG: ssn:SSON_3652 chromosomal replication initiation protein%7ETIGRFAM:
>>
>> I've used
>> bin/flatfile-to-json.pl --gff pyu_file.gff --trackLabel AnnotationsGff --out /opt/apollo/data
>> To add the annotation.
>>
>> I guess I am doing something wrong there, but I cannot seem to figure out what. I am assuming it's the --type and tried several options there, but nothing worked.
>>
>> Thanks,
>> Heleen.
>>
>>
>>
>>
>> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
>> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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