Log.final.out for --quantMode TranscriptomeSAM

[Alexandria Pinto]

Hello Alex,

I am utilizing your --quantMode transcriptomeSAM option and I was wondering, is there a Log.final.out that relates to the transcriptome mapping rate? I have deduced that the Log.final.out file created with the run belongs to the nonTranscriptome alignment BAM.

Alex

[Alexander Dobin]

Hi Alexandria,

there is no statistics output for transcriptomic output - that's a great suggestion, adding it to my TODO list.

For some basic mapping stats you can do samtools flagstat .

Cheers

Alex