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?
I never used CIRI2 but I think you can do the same way as I used to pipe with samtools:
bwa mem genome.fa reads.fastq | samtools sort -O BAM -o output.bam -
So it would be something like:
bwa mem genome.fa reads.fastq | CIRI2 <your options>
I think you will need to precise that CIRI2 input is STDIN. I hope it will help,