Generate indexed genome, chrom size, and res fragment bed for HicPro analysis

usage: hicpro_genome.py [-h] [-j JID] [--interactive] -g GENOME -f
                        GENOME_FASTA [-e DIGESTED_ENZYME]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        hicpro_genome_yli11_2020-06-23)
  --interactive         run pipeline interatively (default: False)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. By default,
                        specifying a genome version will automatically update
                        index file, black list, chrom size and
                        effectiveGenomeSize, unless a user explicitly sets
                        those options. (default: None)
  -f GENOME_FASTA, --genome_fasta GENOME_FASTA
                        please use absolute path (default: None)
  -e DIGESTED_ENZYME, --digested_enzyme DIGESTED_ENZYME
                        digested_fragments (default: MboI)

Summary

Given any genome fasta file and a genome name, this program will create all the necessary inputs for HiC-Pro.

Usage

Note that -f requires absolute PATH to the fasta file.

hpcf_interactive

module load python/2.7.13

hicpro_genome.py -g hg19_20copy -f /home/yli11/dirs/blood_regulome/chenggrp/Projects/hgcOPT_insulator/Data/hg19_new_genome/hg19_20copy.fa

Output

Bowtie2 index, chrom size, and restriction enzyme bed file are inside $jid folder.

Comments

code @ github.