---
name: "umis"
section: "1"
platform: "linux"
package: "umis"
version: "1.0.8-3+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/umis"
---

# umis(1)

tools for processing UMI RNA-tag data

## NAME

umis - tools for processing UMI RNA-tag data

## SYNOPSIS

**umis** \[*OPTIONS*\] *COMMAND* \[*ARGS*\]...

## OPTIONS

- **--help**

  Show this message and exit.

### Commands:

- add\_uid

  Adds UID:\[samplebc cellbc umi\] to readname for...

- bamtag

  Convert a BAM/SAM with fastqtransformed read names to...

- cb\_filter

  Filters reads with non-matching barcodes Expects...

- cb\_histogram

  Counts the number of reads for each cellular barcode...

- demultiplex\_cells

  Demultiplex a fastqtransformed FASTQ file into a...

- demultiplex\_samples

  Demultiplex a fastqtransformed FASTQ file into a...

- fastqtransform

  Transform input reads to the tagcounts compatible...

- fasttagcount

  Count up evidence for tagged molecules, this...

- kallisto

  Convert fastqtransformed file to output format...

- mb\_filter

  Filters umis with non-ACGT bases Expects formatted...

- sb\_filter

  Filters reads with non-matching sample barcodes...

- sparse

  Convert a CSV file to a sparse matrix with rows and...

- subset\_bamfile

  Subset a SAM/BAM file, keeping only alignments from...

- tagcount

  Count up evidence for tagged molecules

- umi\_histogram

  Counts the number of reads for each UMI Expects...

-

  version

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.