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caochch / RIC-seq

Perl scripts for analysis RIC-seq data
GNU General Public License v3.0
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How to clip the poly(N) tails at the 3′ end #2

Closed QianzhaoJ closed 2 years ago

QianzhaoJ commented 3 years ago

Hi, RIC-seq technology is a helpful method to profile global RNA-RNA interactions, and I am very interested in the results showing published paper. So I downloaded RIC-seq data from the GEO database and tried the downstream analysis. I have trimmed adapters and PCR duplicates as paper described, but confused about the steps about clipping the poly(N) tails. I noticed the software cutadapt, but about the parameter settings, could you give me some suggestions? Thanks in advance!

Best wishes Qianzhao

caochch commented 3 years ago

The command looks like this: cutadapt -j 10 -b A{100} -b C{100} -b G{100} -b T{100} ....