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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Export coverage depth RNAseq https://forum.ugene.net/forum/YaBB.pl?num=1396395835 Message started by Adam on Apr 2^nd, 2014 at 6:43am

Title: Export coverage depth RNAseq
Post by Adam on Apr 2^nd, 2014 at 6:43am

Hi,

I understand that there's no feature to export the coverage at each position of the reference. Is there some workaround I can do to get this information? Export as SAM and load into some other (free) program? Or export images and analyse them??

Cheers,

Adam

Title: Re: Export coverage depth RNAseq
Post by Ilya Flyamer on Jun 21^st, 2014 at 3:47am

Export sam (bam) and use samtools: https://www.biostars.org/p/54278/

Title: Re: Export coverage depth RNAseq
Post by Olga Golosova on Jun 25^th, 2014 at 12:03pm

Hello, Adam!
In what format would you like to export the coverage?
Do you need something like specified on the biostars page mentioned by Ilya?

pos A C G T
1 A:2 C:3 G:0 T:1
2 A:2 C:3 G:0 T:1
3 A:0 C:0 G:0 T:7
4 ..
..

May I ask how would you like to use such file? It may help to understand how such feature should be added into UGENE and how popular it is.

Title: Re: Export coverage depth RNAseq
Post by Olga Golosova on Feb 25^th, 2015 at 8:28pm

An update for the current UGENE version 1.16:
1) The coverage can be exported in the Assembly Browser.
2) It can be automated for several assemblies using a sample workflow.