Description

Convert BAM files to cooler format for Hi-C analysis

Input

Name
Description
Pattern

ch_bam_list (file)

The input channel containing a list of BAM files Structure: [ val(meta), [path(bam1), path(bam2), ...] ]

*.bam

ch_chrom_sizes (file)

The input channel containing chromosome sizes file Structure: [ val(meta), path(chrom_sizes) ]

*.{txt,sizes}

val_bin_size (integer)

Bin size for cooler matrix (e.g., 1000)

Output

Name
Description
Pattern

merged_cool (file)

Channel containing merged cooler file Structure: [ val(meta), path(cool) ]

*.cool

mcool (file)

Channel containing multi-resolution cooler file Structure: [ val(meta), path(mcool) ]

*.mcool

Components

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