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Export coverage depth RNAseq (Read 21261 times)
Apr 2nd, 2014 at 6:43am

Adam   Offline
YaBB Newbies

Posts: 2

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??


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Reply #1 - Jun 21st, 2014 at 3:47am

Ilya Flyamer   Offline
Full Member

Gender: male
Posts: 126
Export sam (bam) and use samtools: https://www.biostars.org/p/54278/
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Reply #2 - Jun 25th, 2014 at 12:03pm

Olga Golosova   Offline
YaBB Administrator

Posts: 338
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.
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Reply #3 - Feb 25th, 2015 at 8:28pm

Olga Golosova   Offline
YaBB Administrator

Posts: 338
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.
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