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use name-collated
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veldsla committed Jan 30, 2024
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Expand Up @@ -16,7 +16,7 @@ It is our intention to publish to bioconda soon.
### Input
Coordinate sorted BAM (file or stdin). When paired end reads are used the BAM
file should hve the `MC` and `ms` tags added. This can usually be done by
piping the usually name-sorted bam/sam output from the aligner through
piping the usually name-collated bam/sam output from the aligner through
`samtools fixmate`.

The UMI should be present in the BAM `RX` tag. Because the standard Illumina
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