[Gmod-ajax] Displaying GFF3 isoforms

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[Gmod-ajax] Displaying GFF3 isoforms

grahammb
Hello,

I have a question that I assume is a simple one - yet I cannot get it to work.
I am trying to display a GFF3 file that contains gene information. On the final product, I would like it to display all isoforms that are in the file but I would also like it to have a certain look to it.

For example, in the attached photo, I have one track (TranscriptGFF3) that can display all of the isoforms (Sox17-001 through 008). On a second track (82 GFF3 colored) I have displayed the data how I would like it to look, but notice that isoforms that are small are hidden (such as Sox17-008).

Is there any way to get all isoforms in the first track (from track "TranscriptGFF3") to display like the second track ("82 GFF3 colored").

I think it has to do with how I am running the flatfile-to-json - I ran it like this for the "TranscriptGFF3" track:
bin/flatfile-to-json.pl --gff data/ensembl.mus_musculus/82/genes/Mus_musculus.GRCm38.82.gff3 --tracklabel TranscriptGFF3 --type transcript --out data/ensembl.mus_musculus/82/

Or it is the way I am displaying the tracks, as "TranscriptGFF3" is set as: "trackType" : "CanvasFeatures" while my "82 GFF3 colored" track is a "FeatureTrack".


Any help would be appreciated.

Thank you,
Mitchell Graham


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Re: Displaying GFF3 isoforms

Colin
One reason might be that if you have a GFF that uses the type "transcript" instead of "mRNA" in your GFF (which is implied when you use the flatfile-to-json.pl --type transcript instead of --type mRNA), then you also should set "transcriptType": "transcript" in the track config :)

Here is a related FAQ entry!



-Colin

On Mon, Apr 18, 2016 at 8:58 AM, Graham, Mitchell <[hidden email]> wrote:
Hello,

I have a question that I assume is a simple one - yet I cannot get it to work.
I am trying to display a GFF3 file that contains gene information. On the final product, I would like it to display all isoforms that are in the file but I would also like it to have a certain look to it.

For example, in the attached photo, I have one track (TranscriptGFF3) that can display all of the isoforms (Sox17-001 through 008). On a second track (82 GFF3 colored) I have displayed the data how I would like it to look, but notice that isoforms that are small are hidden (such as Sox17-008).

Is there any way to get all isoforms in the first track (from track "TranscriptGFF3") to display like the second track ("82 GFF3 colored").

I think it has to do with how I am running the flatfile-to-json - I ran it like this for the "TranscriptGFF3" track:
bin/flatfile-to-json.pl --gff data/ensembl.mus_musculus/82/genes/Mus_musculus.GRCm38.82.gff3 --tracklabel TranscriptGFF3 --type transcript --out data/ensembl.mus_musculus/82/

Or it is the way I am displaying the tracks, as "TranscriptGFF3" is set as: "trackType" : "CanvasFeatures" while my "82 GFF3 colored" track is a "FeatureTrack".


Any help would be appreciated.

Thank you,
Mitchell Graham


------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
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Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
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