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Recover unmapped reads #139

Closed HenriettaHolze closed 2 months ago

HenriettaHolze commented 2 months ago

Ask away!

Hi, is it possible to get cell barcode and UMI tagged unmapped reads from the pipeline?

I checked the tagged.bam output file and it does not contain unmapped reads.
I need unmapped reads that are tagged with cell barcode and UMI. Can I modify the pipeline to include unmapped reads in the tagged.bam file? Or is there an intermediate output file in a work directory that has tagged unmapped reads?

Cheers!
Henrietta

nrhorner commented 2 months ago

Hi @HenriettaHolze

Unfortunately the unmapped reads are filtered out just after the mapping step. Additionally, we use the alignment information to cluster reads during the UMI correct step. So it would take quite a bit of hacking of the code to get the data you're after.

Neil