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.
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