Counting overlapping reads

[Vladimir Wischnewski]

Dear all,

Thank you very much for providing this incredible tool.

I have a question related to the in-house RNA-seq processing pipeline.

I was wondering how the internal data processing pipeline handles reads mapping to multiple genes/regions (multi-mapper)?

The GDC pipeline is removing all reads that map to more than one gene, which makes it impossible to study genes with orthologues in the genome. Thus, I was wondering if your in-house processing handle this differently. Unfortunately, I couldn´t find this information in the original publication or the github page.

I look much forward to hearing from you.

All the best,

Vladimir

[Mary Goldman]

Hi Vladimir,

While the UCSC Toil RNAseq recompute was computed at UCSC, it was not computed by the Xena team itself. Our dataset pages may have the answer: https://xenabrowser.net/datapages/?host=https%3A%2F%2Ftoil.xenahubs.net, but if not, you will likely need to contact the corresponding author of the paper, Benedict Paten, or the first author, John Vivian.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[Vladimir Wischnewski]

Hi Mary,

Thank you very much for your quick reply. This info is unfortunately not provided on the dataset pages.

I will contact the  author.

All the best,

Vladimir