Closed aparajitadutta closed 3 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
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.