Description

Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (list)

List of input FASTQ files whose UMIs will be extracted.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

Extracted FASTQ files. | For single-end reads, pattern is ${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is ${prefix}.umi_extract_{1,2}.fastq.gz.

*.{fastq.gz}

log (file)

Logfile for umi_tools

*.{log}

versions (file)

File containing software versions

versions.yml
included in
atacseq callingcards riboseq rnaseq rnasplice smrnaseq
maintainers
Github user drpatelh
Github user grst
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

umi_tools

UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

umi-tools.readthedocs.io/en/latest