Hi,

I'm trying to process the BigWig Files of TCGA patients and access them via the URL provided in the $BigWigURL column of the RangedSummarizedExperiment created with create_rse(). I have three questions:

1) As there is just a single BigWig Url per sample I assume that the coverage of the plus and minus strand are combined. Is this correct? 2) In the case of a stranded RNA-seq library is there a way to obtain separate BigWig files for the plus and minus strand to discriminate between the signal from the plus and minus strand? 3) Is there somewhere information (a column in the colData of the RangedSummarizedExperiment object?) whether the samples are unstranded or stranded?

Thanks in advance!

Best, Mario

Hi Mario,

Thank you for your interest in recount3!

Information across strands is collapsed on these BigWig files and we do not have (and thus don't provide access) to stranded BigWig files. BigWig files compose most of the data storage for the recount2 and recount3 projects, which led to our decision to not double them. AFAIK you can't separate a collapsed BigWig into stranded ones. SPEAQeasy https://doi.org/10.1186/s12859-021-04142-3 does generate stranded BigWigs, but well, it was designed for another purpose.

From http://rna.recount.bio/docs/quality-check-fields.html, I don't think that we have a variable that you can use to differentiate stranded vs unstranded data. I might be missing something that Christopher Wilks might recall, but assume that the answer is no to your third question.

Best, Leo