Feature request for BAM tag on STARSolo

[cnk113]

Hey Alex,

I was wondering if it was possible to get a similar feature from CellRanger which is to tag (RE:) if the reads are intronic (N), exonic (E), or intergenic (I)? I'm assuming this is pulled from the GTF file.

Best,
Chang

[alexdobin]

Hi Chang,

I can output Exonic/Intronic tag for --soloFeatures GeneFull_ExonOverIntron and GeneFull_Ex50pAS.
There is no "intergenic" assessment, the reads that are not intronic or exonic, could be either intergenic or belong to novel transcripts.

Cheers
Alex

[cnk113]

Yeah you're probably right on the intergenic assignment, I'm not too sure how they make that classification, but it's likely the remaining category after assigning exonic/intronic.

[hai178912522]

Is this feature ready? Can 2.7.11a distinguish between exonic, intronic, etc. in bam files?