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alexdobin / STAR

RNA-seq aligner
MIT License
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--quantMode TranscriptomeSAM with STARsolo #869

Open vivekbhr opened 4 years ago

vivekbhr commented 4 years ago

Hi @alexdobin

I want to map 10x data with STAR and output transcriptome alignment separately. When I use --quantMode TranscriptomeSAM, I don't get the cell barcode and the UMI (CB/UB) tags.. Would you suggest how to get this (or implement this feature)?

Additionally, does the --quantTranscriptomeBan feature affect the tx BAM in any way file in star-solo?

Best, Vivek

alexdobin commented 4 years ago

Hi Vivek,

the CB/UB tags output to the Aligned.toTranscriptome.bam file is not implemented yet. I will put it on my list. For now, you can extract these tags from the genomic bam, and attach them to the transcriptomic bam. --quantTranscriptomeBan should work the same way with STARsolo options.

Cheers Alex

vivekbhr commented 4 years ago

Thanks @alexdobin . Yes I am subsetting the genomic BAM for now.. :+1: