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Revert the Split'N'trim step

JCGrenierJCGrenier Montreal, QCMember ✭✭

Hi guys, we are presently building some simulation program in our lab presently and we were wondering if there's already a program known by the community or done by GATK's team to revert back the bam files containing splitted spliced reads like what is outputted by the Split'N'trim step?

I'm asking because we are testing multiple programs to map RNAseq reads and bwa is outputting splitted reads directly and we want to revert them back to reads with N Cigar operators.

Thanks a lot for your help!

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