Description

Regenerate a Pretext contact map after manual curation in PretextView. Corrects the curated AGP onto the input assembly (pretext2asm), remaps Hi-C contacts with juicerc, builds a pairs file (pretext/makepairs), and runs pretextmap.

Input

Name
Description
Pattern

ch_fasta (file)

Input assembly FASTA used for the original Pretext map. Channel shape [ val(meta), path(fasta) ].

*.{fa,fna,fasta}

ch_agp (file)

AGP exported from PretextView after manual curation. Channel shape [ val(meta), path(agp) ] (same meta.id as ch_fasta).

*.agp

ch_hicmap (file)

Hi-C contact file for remapping (Juicer .bin or BAM). Channel shape [ val(meta), path(hicmap) ].

*.{bin,bam}

ch_idxfile (file)

FASTA index (.fai) for the contig-level assembly used in the original Hi-C mapping. Channel shape [ val(meta), path(fai) ].

*.fai

Output

Name
Description
Pattern

pairs (file)

Gzipped pairs file from pretext/makepairs, ready for pretextmap. Channel shape [ val(meta), path(*_alignment.pairs.gz) ].

*_alignment.pairs.gz

pretext (file)

Regenerated Pretext contact map from pretextmap. Channel shape [ val(meta), path(*.pretext) ].

*.pretext

Components

Command copied!