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.