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grexor / apa

apa: research platform for the study of alternative polyadenylation, expressRNA.org
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Scripts for construction of polyA atlas and subsequent filtering steps #16

Closed aparajitadutta closed 3 years ago

aparajitadutta commented 4 years ago

Hi! I have just started looking into the ExpressRNA apa module. I found it interesting and I think the tool will be useful to identify the polyA sites in the human cell line. I have completed the step of mapping and obtained aligned BAM files sorted by coordinates. However I am confused regarding the next steps. I need to iterate over each alignment taking the first (5') nucleotide as a potential polyA cleavage site. Please help me with the script(s) that provides the code for constructing the polyA atlas / database from BAM files by clustering alignment ends (or beginnings, depending on the protocol) and the subsequent filtering steps.

grexor commented 4 years ago

Hello aparajitadutta,

Thank you for trying out expressRNA apa module!

Did you try to run:

apa.polya

Part of the analysis? This module constructs a polyA database from experiments in your library.

Hope this helps, Gregor