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MonashBioinformaticsPlatform / polyApipe

polyApipe
GNU Lesser General Public License v2.1
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UR vs UB umi tag #2

Closed christinedien closed 1 year ago

christinedien commented 1 year ago

Hello!

Thank you for the tool. I got the following error because my BAM files are missing the UR tag:

"Fix by annotating cell barcodes and/or UMIs in tags in bam file, and specifying the tags with"+
        " (--cell_barcode_tag / --umi_tag)")

They do have the UB tag though. Is there a reason the UMI tag needs to be the uncorrected version? Would it be appropriate to set --umi_tag to UB?

Thank you!

pfh commented 1 year ago

Hi!

polyApipe.py uses umi_tools to count UMIs associated with peaks. This has its own UMI clustering method, so there is no need for corrected barcodes. However, I can't imagine there would be any harm using the corrected barcode. Using UB should be fine.