Question: bam to stranded bigwig?
0
gravatar for elizabeth.bayne
6 months ago by
elizabeth.bayne10 wrote:

Hi, I have a bam file generated from stranded RNA-seq data - is it possible to use galaxy to split this bam file into two bigwig (or similar) files, one for each strand?

rna-seq bam • 243 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by elizabeth.bayne10
1
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Try the tool DeepTools: bamCoverage. On the tool form, under "advanced options", are settings that can apply strand filters.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson23k
1

Fantastic - got it, thank you!

ADD REPLYlink written 6 months ago by elizabeth.bayne10
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