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Display read depth

asked 2018-05-08 17:32:06 -0500

gpharhay gravatar image

updated 2018-05-09 17:08:36 -0500

Hi: I would like to overlay RNA-seq data in the genome browser. Is this possible? If not, is there a mechanism to display read depth in the genome browser. Something like a track in the genome browser that would show coverage vs genome position? If so, would this be visualized in both the desktop and web version of ptools? Thanks.

Bedtools has a pretty slick utility that converts a BAM files to genome read coverage as described in http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html?highlight=genomecov (genomecov)

I could convert a BAM file of RNA-seq data to a http://genome.ucsc.edu/goldenPath/help/bedgraph.html (bedgraph) format

chr1 554304 554309 25

(chromA chromStartA chromEndA dataValueA, where dataValueA is read coverage)

and then stuff text into each line to convert to something GFF2 like

chr1 rna-seq cover 554304 554309 25

which presumably could be ingested into ptools and displayed as a Track. That got me thinking that the extra columns in the GFF2, although necessary for GFF2, really are not informative in this use case. That my way of trying to convince SRI to tweak ptools to accept bedgraph format files.

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answered 2018-05-09 09:34:12 -0500

Suzanne Paley gravatar image

You as a user of the database can upload a data file and display it as a track on the genome browser on both web and desktop versions (navigate to the genome browser and look for the Show Tracks button), so if all you want to do is generate a figure for your poster you should be fine. However, there is currently no way that you as a database curator can add a data track that is then visible to users, and there is no way to add a track based on data stored somewhere in the database, if that's what you were hoping to do.

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Asked: 2018-05-08 17:32:06 -0500

Seen: 1,420 times

Last updated: May 09