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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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UMI-collapsed BAM #359

Open gevro opened 1 year ago

gevro commented 1 year ago

Hi, Is the output BAM contain all UMI reads from each molecule, or only one UMI-collapsed read from each unique UMI molecule? If the former, is there a way to generate a "collapsed" BAM that retains only a single read from each UMI?

cziegenhain commented 1 year ago

The output BAM file contains all reads. There is no option to generate a file with consensus/collapsed reads.

gevro commented 1 year ago

Does the gene counting / expression analysis take into account UMIs I assume? i.e., it only counts each molecule once, even if > 1 read per UMI?

cziegenhain commented 1 year ago

You receive a count table with both read counts and unique UMI counts. https://github.com/sdparekh/zUMIs/wiki/Output#structure-of-the-output-dgecounts-object-in-project_namedgecountsrds