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

Question

[Lila M]

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!

[WouterDeCoster]

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

Answer 1

[Istvan Albert]

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?