Description

Build contact maps from pairs files using PretextMap, Juicertools, and Cooler

Input

Name
Description
Pattern

ch_pairs (file)

Input Hi-C pairs in pairs format (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md).

Structure: [ val(meta), path(pairs) ]

*.pairs.gz

ch_chrom_sizes (file)

Input chromosome sizes file - a TSV with two columns, name and size.

Structure: [ val(meta), path(sizes) ]

*.{sizes,tsv}

ch_pretext_snapshot_order_file (file)

Input custom order file - a txt file of new line separated chromosome names.

Structure: [ val(meta), path(order) ]

*.{txt}

val_build_pretext (boolean)

Build a PretextMap contact map

val_create_pretext_snapshot (boolean)

Create a snapshot of the PretextMap contact map

val_build_cooler (boolean)

Build a Cooler contact map

val_build_juicer (boolean)

Build a Juicer contact map

val_cool_bin (integer)

Bin size for cooler

Output

Name
Description
Pattern

pretext (file)

Contact map in PretextMap format. Structure: [ val(meta), path(pretext) ]

*.pretext

pretext_png (file)

PNG visualisation of the Pretext contact map. Structure: [ val(meta), path(png) ]

*.png

cool (file)

Contact map in mCooler format Structure: [ val(meta), path(mcool) ]

*.mcool

hic (file)

Contact map in Juicer format Structure: [ val(meta), path(hic) ]

*.hic

Components

Command copied!