Description

Convert annotated Long-C monomer BAM alignments to .pairs.gz using pairtools parse2, streaming output through bgzip.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam (file)

Annotated, coordinate-sorted BAM with FI, FD, and BX tags from Long-C fragment annotation.

*.bam

chromsizes (file)

Chromosome sizes file for the reference assembly (e.g. from samtools faidx)

*.{sizes,fa.fai,fai}

Output

Name
Description
Pattern

pairs

meta (map)

Groovy Map containing sample information

*.pairs.gz (file)

Gzipped pairs file from pairtools parse2 (bgzip-compressed)

*.pairs.gz

versions_pairtools

${task.process} (string)

The process the versions were collected from

pairtools (string)

The tool name

pairtools --version | sed 's/.*pairtools.*version //' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

pairtools (string)

The tool name

pairtools --version | sed 's/.*pairtools.*version //' (eval)

The expression to obtain the version of the tool

Tools

pairtools Documentation

CLI tools to process mapped Hi-C and chromatin conformation data; parse2 reports ligation junctions from complex walks in annotated alignments.

https://github.com/open2c/pairtoolsLicense: MIT
Authors