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alexdobin / STAR

RNA-seq aligner

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Question about --outSAMmultNmax and TranscriptomeSAM

andresferben opened this issue · comments

commented

Hi there,

It looks like the --outSAMmultNmax option does not affect the transcriptome BAM (generated with --quantMode TranscriptomeSAM). Is this correct?
Is there a way to make it work? I need to get only the best alignment per read, which is achieved with --outSAMmultNmax 1 for the genome BAM but not for the transcriptome.

Thanks