run_hicpro: run the hic-pro

In HBP: Hi-C BED File Analysis Pipeline

Description

help users to map and normalize Hi-C raw dataset by HiC-Pro

Arguments

hicpro_path	if the path of HiC-Pro is already added to environment PATH, you can use hicpro_path = "HiC-Pro"
inputfile	the raw fastq data file folder. for example, my Hi-C data sequencing file is myhic_R1.fastq and myhic_R2,fastq, they should be placed in ../rawdata/myhic/myhic_R1.fastq and ../rawdata/myhic/myhic_R2.fastq.
configfile	the HiC-Pro config file, there is a example file in https://github.com/hechao0407/HBP/blob/master/config-hicpro.txt.
outdir	the output folder of this function

Details

this function is used to help users to map and normalize Hi-C raw dataset by HiC-Pro. HiC-Pro can be download at http://github.com/nservant/HiC-Pro

HBP documentation built on July 7, 2017, 9:02 a.m.