run_hicpro

if the path of HiC-Pro is already added to environment PATH, you can use hicpro_path = "HiC-Pro"

hicpro_path

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.

inputfile

the HiC-Pro config file, there is a example file in https://github.com/hechao0407/HBP/blob/master/config-hicpro.txt.

configfile

the output folder of this function

outdir

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

 ~kwd1 

 ~kwd2 

Hi-C dataset processing algorithm introduced by Chao He (2016) <doi.org/10.1101/083576>.
The optimized and flexible pipeline for analyzing the
folding of whole chromosome and interactions between some
specific sites from the Hi-C raw sequencing reads to the
partially processed datasets. The other complex genetic and
epigenetic datasets from public sources such as GWAS, ENCODE
consortiums etc. will also easily be integrated into HBP,
hence the final output results of HBP could provide a
comprehensive in-depth understanding for the specific
chromatin interactions, potential molecular mechanisms and
biological significance. We believe that HBP is a reliable
tool for the rapidly analysis of Hi-C data and will be very
useful for a wide range of researchers, particularly those
who lack of background in computational biology.

run_hicpro: run the hic-pro

Description

Arguments

Details