Question: Run CIRI program directly from BWA-mem alignment
gravatar for onjinakashima
11 months ago by
onjinakashima0 wrote:

Hello, I'm trying to find circular ARN using the program CIRI2. CIRI2 takes as input SAM file from BWA-mem, but I would like to go straight to CIRI2 output without saving SAM file. Is there a way to achieve this?

rna-seq alignment • 405 views
ADD COMMENTlink written 11 months ago by onjinakashima0

You could try process substitution for the input sam perl -I <(put your bwa mem call (or even bwa mem | samtools pipeline) here) -O outfile -F ref.fa (-R ref_dir/) -P. It is not guaranteed to work, though, especially if CIRI makes multiple passes over the sam file.

ADD REPLYlink written 11 months ago by cschu1811.4k
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