[Gmod-ajax] GeneID instead of ID on the genome browser?

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[Gmod-ajax] GeneID instead of ID on the genome browser?

Raymond Wan-2
Dear all,

Given a GFF3 file formatted as follows:

...
##gff-version 3
chr1    stdin    mRNA    3204563    3661579    .    -    .
ID=NM_001011874;geneID=Xkr4;gene_name=Xkr4
...


In the genome browser, I can see the NM identifier.  If I click on the
feature, then it says that the gene ID is Xkr4 in the pop-up window.

Is there a way to display "Xkr4" (i.e., the gene's name) in the
browser instead of the NM identifier?  I was thinking of changing my
GFF3 file so that the IDs are removed and the geneID becomes the ID,
but I worry that I will encounter other problems.  For example,
duplicate gene names (I presume the NM identifiers have a better
chance of being unique?).

Incidentally, I have a GTF file with this already done to it and when
I ran Cufflinks' gffread on it, it converted it to the above format.
i.e.,

it took this:

chr1    unknown    exon    3204563    3207049    .    -    .
gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id
"NM_001011874"; tss_id "TSS1978";

and changed it to this:

chr1    unknown    mRNA    3204563    3661579    .    -    .
ID=NM_001011874;geneID=Xkr4;gene_name=Xkr4;p_id=P1298;tss_id=TSS1978

Indeed, I *think* I can play with GTF file in such a way that the
gffread program could output ID=Xkr4, but I have this feeling I'm
going about it wrong.  And if both the geneID and ID are already
stored by JBrowse, I guess there is a way to modify the track
configuration to show the former instead of the latter?

Any suggestions would be appreciated!  Thank you!

Ray

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Re: GeneID instead of ID on the genome browser?

vkrishna
Hi Raymond,

The functionality you are looking for is already present and would not require altering the input GFF3 format file.

In JBrowse, each feature has 2 “display” attributes, a short “label" and a long “description”, which are shown beneath a feature glyph. These are controlled within the “style” stanza of a given track configuration.

By default, style->label is pulled from the following 9th column fields: 'name,id’, whichever is available first. The style->description is pulled from the following 9-th column fields: ‘description,note’. Please see docs: http://gmod.org/wiki/JBrowse_Configuration_Guide#HTMLFeatures_Configuration_Options

In your case, you can set style->label: ‘geneid,name,id’, which sets the priority and will display the content of the “geneID” attribute when available, and use the ID attribute to fall back when “geneID” isn’t present.

Hope this helps!

Thank you.

Regards,
Vivek

> On Feb 15, 2016, at 10:15 PM, Raymond Wan <[hidden email]> wrote:
>
> Dear all,
>
> Given a GFF3 file formatted as follows:
>
> ...
> ##gff-version 3
> chr1    stdin    mRNA    3204563    3661579    .    -    .
> ID=NM_001011874;geneID=Xkr4;gene_name=Xkr4
> ...
>
>
> In the genome browser, I can see the NM identifier.  If I click on the
> feature, then it says that the gene ID is Xkr4 in the pop-up window.
>
> Is there a way to display "Xkr4" (i.e., the gene's name) in the
> browser instead of the NM identifier?  I was thinking of changing my
> GFF3 file so that the IDs are removed and the geneID becomes the ID,
> but I worry that I will encounter other problems.  For example,
> duplicate gene names (I presume the NM identifiers have a better
> chance of being unique?).
>
> Incidentally, I have a GTF file with this already done to it and when
> I ran Cufflinks' gffread on it, it converted it to the above format.
> i.e.,
>
> it took this:
>
> chr1    unknown    exon    3204563    3207049    .    -    .
> gene_id "Xkr4"; gene_name "Xkr4"; p_id "P1298"; transcript_id
> "NM_001011874"; tss_id "TSS1978";
>
> and changed it to this:
>
> chr1    unknown    mRNA    3204563    3661579    .    -    .
> ID=NM_001011874;geneID=Xkr4;gene_name=Xkr4;p_id=P1298;tss_id=TSS1978
>
> Indeed, I *think* I can play with GTF file in such a way that the
> gffread program could output ID=Xkr4, but I have this feeling I'm
> going about it wrong.  And if both the geneID and ID are already
> stored by JBrowse, I guess there is a way to modify the track
> configuration to show the former instead of the latter?
>
> Any suggestions would be appreciated!  Thank you!
>
> Ray
>
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Re: GeneID instead of ID on the genome browser?

Raymond Wan-2
Hi Vivek,


On Tue, Feb 16, 2016 at 11:26 AM, Krishnakumar, Vivek <[hidden email]> wrote:
> The functionality you are looking for is already present and would not require altering the input GFF3 format file.
>
> In JBrowse, each feature has 2 “display” attributes, a short “label" and a long “description”, which are shown beneath a feature glyph. These are controlled within the “style” stanza of a given track configuration.
>
> By default, style->label is pulled from the following 9th column fields: 'name,id’, whichever is available first. The style->description is pulled from the following 9-th column fields: ‘description,note’. Please see docs: http://gmod.org/wiki/JBrowse_Configuration_Guide#HTMLFeatures_Configuration_Options
>
> In your case, you can set style->label: ‘geneid,name,id’, which sets the priority and will display the content of the “geneID” attribute when available, and use the ID attribute to fall back when “geneID” isn’t present.
>
> Hope this helps!


Perfect!  Thank you for the detailed explanation and the pointer to
the documentation!

In the docs, it says the default is "name,id" -- I presume that didn't
work out for me because my data file has the gene names in the field
"gene_name" instead of "name".  Otherwise, the default setting would
have worked.

Thanks you for saving me the trouble of writing some script to mess up
the GFF3 file!  :-)

Sorry to ask yet another question but not sure if you or anyone else
knows...  Is it possible to index the gene_name or any field other
than the ID field (again, without playing with the GFF3 file)?  I
think bin/generate-names.pl only indexes the ID...but I'm not too
sure.

Thank you!

Ray

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Re: GeneID instead of ID on the genome browser?

Colin
Hi Raymod,

I think the default fields that are indexed are Name, ID, and Alias fields, but I think you can change that when you load the track with flatfile-to-json.pl in the first place by using the "nameAttributes" argument

I tested out adding, say, a gene_id field to a GFF, and then loaded it with

$ flatfile-to-json.pl --nameAttributes "name,id,alias,gene_id"  ...

And then after running generate-names.pl, it picked up the gene_id field in the search box

That --nameAttributes setting is actually news to me but I hope that helps :)

-Colin

On Mon, Feb 15, 2016 at 9:48 PM, Raymond Wan <[hidden email]> wrote:
Hi Vivek,


On Tue, Feb 16, 2016 at 11:26 AM, Krishnakumar, Vivek <[hidden email]> wrote:
> The functionality you are looking for is already present and would not require altering the input GFF3 format file.
>
> In JBrowse, each feature has 2 “display” attributes, a short “label" and a long “description”, which are shown beneath a feature glyph. These are controlled within the “style” stanza of a given track configuration.
>
> By default, style->label is pulled from the following 9th column fields: 'name,id’, whichever is available first. The style->description is pulled from the following 9-th column fields: ‘description,note’. Please see docs: http://gmod.org/wiki/JBrowse_Configuration_Guide#HTMLFeatures_Configuration_Options
>
> In your case, you can set style->label: ‘geneid,name,id’, which sets the priority and will display the content of the “geneID” attribute when available, and use the ID attribute to fall back when “geneID” isn’t present.
>
> Hope this helps!


Perfect!  Thank you for the detailed explanation and the pointer to
the documentation!

In the docs, it says the default is "name,id" -- I presume that didn't
work out for me because my data file has the gene names in the field
"gene_name" instead of "name".  Otherwise, the default setting would
have worked.

Thanks you for saving me the trouble of writing some script to mess up
the GFF3 file!  :-)

Sorry to ask yet another question but not sure if you or anyone else
knows...  Is it possible to index the gene_name or any field other
than the ID field (again, without playing with the GFF3 file)?  I
think bin/generate-names.pl only indexes the ID...but I'm not too
sure.

Thank you!

Ray

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Re: GeneID instead of ID on the genome browser?

Raymond Wan-2
Hi Colin,

Thanks for this!  Vivek mentioned something similar and I just
realized that the mailing list was not copied in his original reply.
Sorry about that!

Indeed, I was not aware of that option and relied a bit too much on
"default values" when I ran flatfile-to-json.pl .  I was in the midst
of digging through generate-names.pl ... I'm thankful that both of you
saved me the trouble since that would have been the entirely wrong
direction!

I'll give what you suggest a try in a couple of days as something else
has suddenly distracted me.  But given that you've tried it, it should
surely work.  Thanks for your follow-up!

Ray




On Sun, Feb 21, 2016 at 8:28 AM, Colin <[hidden email]> wrote:

> Hi Raymod,
>
> I think the default fields that are indexed are Name, ID, and Alias fields,
> but I think you can change that when you load the track with
> flatfile-to-json.pl in the first place by using the "nameAttributes"
> argument
>
> I tested out adding, say, a gene_id field to a GFF, and then loaded it with
>
> $ flatfile-to-json.pl --nameAttributes "name,id,alias,gene_id"  ...
>
> And then after running generate-names.pl, it picked up the gene_id field in
> the search box
>
> That --nameAttributes setting is actually news to me but I hope that helps
> :)
>
> -Colin
>
> On Mon, Feb 15, 2016 at 9:48 PM, Raymond Wan <[hidden email]> wrote:
>>
>> Hi Vivek,
>>
>>
>> On Tue, Feb 16, 2016 at 11:26 AM, Krishnakumar, Vivek <[hidden email]>
>> wrote:
>> > The functionality you are looking for is already present and would not
>> > require altering the input GFF3 format file.
>> >
>> > In JBrowse, each feature has 2 “display” attributes, a short “label" and
>> > a long “description”, which are shown beneath a feature glyph. These are
>> > controlled within the “style” stanza of a given track configuration.
>> >
>> > By default, style->label is pulled from the following 9th column fields:
>> > 'name,id’, whichever is available first. The style->description is pulled
>> > from the following 9-th column fields: ‘description,note’. Please see docs:
>> > http://gmod.org/wiki/JBrowse_Configuration_Guide#HTMLFeatures_Configuration_Options
>> >
>> > In your case, you can set style->label: ‘geneid,name,id’, which sets the
>> > priority and will display the content of the “geneID” attribute when
>> > available, and use the ID attribute to fall back when “geneID” isn’t
>> > present.
>> >
>> > Hope this helps!
>>
>>
>> Perfect!  Thank you for the detailed explanation and the pointer to
>> the documentation!
>>
>> In the docs, it says the default is "name,id" -- I presume that didn't
>> work out for me because my data file has the gene names in the field
>> "gene_name" instead of "name".  Otherwise, the default setting would
>> have worked.
>>
>> Thanks you for saving me the trouble of writing some script to mess up
>> the GFF3 file!  :-)
>>
>> Sorry to ask yet another question but not sure if you or anyone else
>> knows...  Is it possible to index the gene_name or any field other
>> than the ID field (again, without playing with the GFF3 file)?  I
>> think bin/generate-names.pl only indexes the ID...but I'm not too
>> sure.
>>
>> Thank you!
>>
>> Ray
>>
>>
>> ------------------------------------------------------------------------------
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>> Monitor end-to-end web transactions and take corrective actions now
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

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Re: GeneID instead of ID on the genome browser?

Raymond Wan-2
In reply to this post by Colin
Hi Colin and Vivek,

Just wanted to confirm what Colin found out through his tests -- yes, it worked!

Thank you for looking into it and letting me know about it!  I
definitely should look into those default options more carefully in
the future...  Thank you!

Ray



On Sun, Feb 21, 2016 at 8:28 AM, Colin <[hidden email]> wrote:

> Hi Raymod,
>
> I think the default fields that are indexed are Name, ID, and Alias fields,
> but I think you can change that when you load the track with
> flatfile-to-json.pl in the first place by using the "nameAttributes"
> argument
>
> I tested out adding, say, a gene_id field to a GFF, and then loaded it with
>
> $ flatfile-to-json.pl --nameAttributes "name,id,alias,gene_id"  ...
>
> And then after running generate-names.pl, it picked up the gene_id field in
> the search box
>
> That --nameAttributes setting is actually news to me but I hope that helps
> :)
>
> -Colin
>
> On Mon, Feb 15, 2016 at 9:48 PM, Raymond Wan <[hidden email]> wrote:
>>
>> Hi Vivek,
>>
>>
>> On Tue, Feb 16, 2016 at 11:26 AM, Krishnakumar, Vivek <[hidden email]>
>> wrote:
>> > The functionality you are looking for is already present and would not
>> > require altering the input GFF3 format file.
>> >
>> > In JBrowse, each feature has 2 “display” attributes, a short “label" and
>> > a long “description”, which are shown beneath a feature glyph. These are
>> > controlled within the “style” stanza of a given track configuration.
>> >
>> > By default, style->label is pulled from the following 9th column fields:
>> > 'name,id’, whichever is available first. The style->description is pulled
>> > from the following 9-th column fields: ‘description,note’. Please see docs:
>> > http://gmod.org/wiki/JBrowse_Configuration_Guide#HTMLFeatures_Configuration_Options
>> >
>> > In your case, you can set style->label: ‘geneid,name,id’, which sets the
>> > priority and will display the content of the “geneID” attribute when
>> > available, and use the ID attribute to fall back when “geneID” isn’t
>> > present.
>> >
>> > Hope this helps!
>>
>>
>> Perfect!  Thank you for the detailed explanation and the pointer to
>> the documentation!
>>
>> In the docs, it says the default is "name,id" -- I presume that didn't
>> work out for me because my data file has the gene names in the field
>> "gene_name" instead of "name".  Otherwise, the default setting would
>> have worked.
>>
>> Thanks you for saving me the trouble of writing some script to mess up
>> the GFF3 file!  :-)
>>
>> Sorry to ask yet another question but not sure if you or anyone else
>> knows...  Is it possible to index the gene_name or any field other
>> than the ID field (again, without playing with the GFF3 file)?  I
>> think bin/generate-names.pl only indexes the ID...but I'm not too
>> sure.
>>
>> Thank you!
>>
>> Ray
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>> _______________________________________________
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

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