Description

Remap Hi-C alignments onto a curated AGP with juicer pre, sort pairs, and filter invalid coordinates — equivalent to the zippypretext juicerc.sh wrapper.

Input

Name
Description
Pattern

meta (map)

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

hicmap (file)

Hi-C alignment file (BAM or Juicer .bin contacts)

*.{bam,bin}

agpfile (file)

AGP file describing scaffold coordinates (typically output of pretext2asm)

*.agp

idxfile (file)

FASTA index (.fai) matching the contig-level Hi-C assembly

*.fai

Output

Name
Description
Pattern

outlog

juicercout.log (file)

Log file written by juicerc.sh

juicercout.log

alignment

meta (map)

Groovy Map containing sample information

*_alignment_sorted.txt (file)

Sorted Hi-C alignment records remapped to scaffold coordinates

*_alignment_sorted.txt

versions_juicerc

${task.process} (string)

The process the versions were collected from

juicerc (string)

The tool name

1.2 (string)

The version of the tool

versions_juicer_pre

${task.process} (string)

The process the versions were collected from

juicer_pre (string)

The tool name

juicer pre --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

juicer_pre (string)

The tool name

juicer pre --version (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

juicerc (string)

The tool name

1.2 (string)

The expression to obtain the version of the tool

Tools

juicer_pre Documentation

Remap Hi-C contacts from a .bin or BAM onto scaffold coordinates in an AGP using a contig-level FASTA index (juicer pre -q 0).

License: MIT
Authors