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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?

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    $\begingroup$ This is an English language list. Do you by any chance mean RNA rather than ARN? And although I may be wrong, I think you are more likely to get an answer on SE Bioinformatics than here. $\endgroup$ – David Jan 13 '18 at 18:44
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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,

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