Hi, am currently trying to call chimeric transcripts from RNASeq data. For this I obtained bam files, sorted them via samtools -n and used picard SamToFastq to convert the bams into fastqs.

This worked fine and I could call fusions. Lately however, I was adviced to set INCLUDE_NON_PF_READS=true and INCLUDE_NON_PRIMARY_ALIGNMENTS=true and re-run the conversion and call for fusions again.

Is this logic? As far as I understand it, INCLUDE_NON_PRIMARY_ALIGNMENTS=true would also include reads that do not map perfectly. And this might be the reads I am interested in, because they might map to distant sites and thereby be discordant.

Thanks for your help!

Best,

Paso.