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dexseq_count.py: strandness of data from portal.gdc.cancer.gov

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 dexseq_count tcga
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updated by Istvan Albert Istvan Albert • written by Lila M Lila M

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

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written by WouterDeCoster WouterDeCoster

1 answer

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?

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written by Istvan Albert Istvan Albert

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