Description

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file containing reads to be deduplicated via UMIs.

*.{bam}

bai (file)

BAM index files corresponding to the input BAM file.

*.{bai}

get_output_stats (boolean)

Whether or not to generate output stats.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file with deduplicated UMIs.

*.{bam}

log (file)

File with logging information

*.{log}

tsv_edit_distance (file)

Reports the (binned) average edit distance between the UMIs at each position.

*edit_distance.tsv

tsv_per_umi (file)

UMI-level summary statistics.

*per_umi.tsv

tsv_umi_per_position (file)

Tabulates the counts for unique combinations of UMI and position.

*per_position.tsv

versions (file)

File containing software versions

versions.yml
included in
nascent radseq riboseq rnaseq scnanoseq
maintainers
Github user drpatelh
Github user grst
Github user klkeys
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