quantMode "TranscriptomeSAM" and outSAMattributes

[dincarnato]

Hi Alex,

hope you are well.

I have a small question/request: when running STAR with quantMode "TranscriptomeSAM", the resulting transcriptome BAM file misses the SAM attributes specified with outSAMattributes. So, it seems like outSAMattributes only affects the genome BAM file. Would it be possible to have control also over the SAM attributes of the transcriptome BAM file (i.e. MD,nM, etc.)?

Many thanks!
All the best,

Danny

[alexdobin]

Hi Danny,

I have this on my TODO list...
In the meantime you can run samtools calcmd command to add MD and NM attributes.

[dincarnato]

Hi Alex,

thanks for your reply.
Indeed that's what I'm doing now, but glad to hear that's on your roadmap!

All the best,
Danny