Skip to content

Latest commit

 

History

History
145 lines (124 loc) · 4.32 KB

HiC_Pro workflow.md

File metadata and controls

145 lines (124 loc) · 4.32 KB
Raw

First attempt to use HiC-Pro to finish a 3D genome analysis HiCPro document: http://nservant.github.io/HiC-Pro/

Content

  1. Install HiC-Pro and dependencies
  2. Download data and preprocess
  3. Setting the configuration file
  4. About the output
  5. Visualization with HiCPlotter

1. Install HiC-Pro and dependencies

1.1 Install dependencies

What we need for hicpro

Dependency function
bowtie2 index
Python (>2.7 & <3) with 4 packages following
pysam (>=0.8.3)
bx-python(>=0.5.0)
numpy(>=1.8.2)
scipy(>=0.15.1)
R with packages RColorBrewer and ggplot2 (>2.2.1)
g++ compiler use "which" to check if we have
samtools (>1.1)

how to install

  1. python pip
  2. conda: the most convenient

1.2 Download HiC-Pro

mkdir -p ~/biosoft/hicpro
cd ~/biosoft/hicpro
git clone https://github.com/nservant/HiC-Pro.git

1.3 System configuration

  • to edit the config-install.txt file and manually defined the paths to dependencies
cat config-install.txt

# edit 
PREFIX =/home/zengjianming/biosoft/hicpro/bin
BOWTIE2_PATH =/home/zengjianming/miniconda3/envs/hic/bin/bowtie2
SAMTOOLS_PATH =/home/zengjianming/miniconda3/envs/hic/bin/samtools
R_PATH =/home/zengjianming/miniconda3/envs/hic/bin/R
PYTHON_PATH =/home/zengjianming/miniconda3/envs/hic/bin/python
CLUSTER_SYS =TORQUE # Resource management system of our server

# install
make configure
make install

# add hicpro to $PATH
vim .bashrc
export HICPRO_PATH=/public/home/liuj626/tools/biosoft/hicpro/bin/HiC-Pro_2.11.1/bin
export PATH=$HICPRO_PATH:$PATH

# check if install successfully 
HiC-Pro -h

2. Download data and preprocess

  • Two parts: Experiment data and Reference genome

2.1 Experiment data

Article:3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations.Nature Communications SRX: SRX2208970 SRR: SRR4341901-SRR4341904

  • ==download sra toolkit==
# use sratool
prefetch SRR4341901

# transform to fa.gz
# sample must be placed in the same folder
fastq-dump --gzip --split-3 SRR4341901

2.2 Reference genome

hg19

  • to prepare .bed and genome size files

.bed file

$ cd /your/path/of/reference/
$ wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
$ tar zvfx chromFa.tar.gz

# Notice that the download file is seperated in different chr
$ cat *.fa > hg19.fa
$ rm chr*.fa

# bowtie2 index：add bowtie2 to path before
$ bowtie2-build hg19.fa hg19.fa
# first "hg19.fa":input file; Second "hg19.fa": prefix of output file
# generate 6 ".bt2"

# .bed 
mkdir -p ~/data/project/hic/digest  # create new folder
cd ~/data/project/hic/digest

bin=/public/.../HiC-Pro_2.10.0/HiC-Pro/bin/utils/digest_genome.py  # use digest_genome.py to generate .bed file
$bin -r C^CATGG  -o  hg19.bed ../ref/hg19.fa

genome size

  • If you use hg19 as reference, hicpro provides some config files(like chrom_hg19.sizes)

3. Setting the configuration file and Run

**every time you run the pipeline you should create a configuration file.**See the manual for details about the configuration file

Step1: edit your config file

  1. Copy and edit the configuration file "config-hicpro.txt" in your local folder.
  2. Put all input files in a rawdata folder. The input files have to be organized with a folder per sample.
  3. Use qsub to submit your pbs script

I have provide my file as example (see)

# the basic context of config file
HiC-Pro -i FULL_PATH_TO_RAW_DATA -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE -p

Step2: qsub the files generated

  • You will get message like this and do as the guidance.
Please run HiC-Pro in two steps :
1- The following command will launch the parallel workflow through 12 torque jobs:
qsub HiCPro_step1.sh
2- The second command will merge all outputs to generate the contact maps:
qsub HiCPro_step2.sh

4. Results

  • The results provide:
  1. mapping results
  2. contact map(matrix form)

5. Visualization with HiCPlotter

Install HiCPlotter

kcakdemir/HiCPlotter: https://github.com/kcakdemir/HiCPlotter/releases

Visualization

  • Notice that the output(.png) will be placed in home directory instead of the working directory(Still don't find solution)
  • It has lots of optional parameters
  • I have uploaded my file as example (see:)
# basic grammar
python HiCPlotter.py -f file -n name -chr chrX -o output