Question: dexseq_count.py: strandness of data from portal.gdc.cancer.gov
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gravatar for Lila M
21 months ago by
Lila M 460
UK
Lila M 460 wrote:

Hi everybody, I'm working with some bam files from https://portal.gdc.cancer.gov/. As I want to perform a differential exon usage analysis dexseq_count.py), I would like to know the strandedness parameters that I should use, as I don't know if the bioportal used a library preparation protocol that preserve strand information or not.

Does any one know about this?

Thanks!

dexseq_count tcga dexseq • 476 views
ADD COMMENTlink modified 21 months ago by Istvan Albert ♦♦ 79k • written 21 months ago by Lila M 460

I edited your title to better reflect what you are asking for.

ADD REPLYlink written 21 months ago by WouterDeCoster37k
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gravatar for Istvan Albert
21 months ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

You can determine the strandedness of a data by visual inspection. I am sure there are tools to do that as well. See this post:

A: How to know that your RNA-seq is stranded or not?

ADD COMMENTlink written 21 months ago by Istvan Albert ♦♦ 79k
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