Run CIRI program directly from BWA-mem alignment

Question

[onjinakashima]

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?

[cschu181]

You could try process substitution for the input sam perl CIRI.pl -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.