This page is just a quick start guide, please read the full online manual for more information !
See NEWS for information about changes in this and previous versions
See LOGBOOK for details about the HiC-Pro developments
See LICENSE for license information
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro can analyse data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C.
The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler. HiC-Pro is sequential and each step of the workflow can be run independantly.
HiC-Pro includes a fast implementatation of the ICE normalization method (see the iced python library for more information).
In addition, HiC-Pro can use phasing data to build
The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler. HiC-Pro is sequential and each step of the workflow can be run independantly.
HiC-Pro includes a fast implementatation of the ICE normalization method (see the iced python library for more information).
In addition, HiC-Pro can use phasing data to build
allele specific contact maps <AS>.If you use HiC-Pro, please cite :
HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Servant N., Varoquaux N., Lajoie BR., Viara E., Chen CJ., Vert JP., Dekker J., Heard E., Barillot E. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x http://www.genomebiology.com/2015/16/1/259
For any question about HiC-Pro, please contact [email protected]
The HiC-Pro pipeline requires the following dependencies :
- The bowtie2 mapper
- Python (>2.7) with pysam, bx, numpy, and scipy libraries
- R with the RColorBrewer and ggplot2 packages
- g++ compiler
- Samtools (>0.1.19)
Bowtie >2.2.2 is strongly recommanded for allele specific analysis. | To install HiC-Pro:
tar -zxvf HiC-Pro-master.tar.gz
cd HiC-Pro-master
make CONFIG_SYS=config-install.txt installNote that if some of these dependencies are not installed (i.e. not detected in the $PATH), HiC-Pro will try to install them.
You can also edit the config-install.txt file and manually defined the paths to dependencies.
You can also edit the config-install.txt file and manually defined the paths to dependencies.
| SYSTEM CONFIGUR | ATION |
|---|---|
| PREFIX | Installation path |
| BOWTIE2_PATH | Full path the bowtie2 installation directory |
| SAMTOOLS_PATH | Full path to the samtools installation directory (>0.1.19) |
| R_PATH | Full path to the R installation directory |
| PYTHON_PATH | Full path to the python installation directory (>2.7) |
In order to process the raw data, HiC-Pro requires three annotation files. Note that the pipeline is provided with some Human and Mouse annotation files.
- A BED file of the restriction fragments after digestion. This file depends both of the restriction enzyme and the reference genome. See the
FAQ <FAQ>and theHiC-Pro utilities <UTILS>for details about how to generate this file. A few annotation files are provided with the HiC-Pro sources.
chr1 0 16007 HIC_chr1_1 0 +
chr1 16007 24571 HIC_chr1_2 0 +
chr1 24571 27981 HIC_chr1_3 0 +
chr1 27981 30429 HIC_chr1_4 0 +
chr1 30429 32153 HIC_chr1_5 0 +
chr1 32153 32774 HIC_chr1_6 0 +
chr1 32774 37752 HIC_chr1_7 0 +
chr1 37752 38369 HIC_chr1_8 0 +
chr1 38369 38791 HIC_chr1_9 0 +
chr1 38791 39255 HIC_chr1_10 0 +
(...)- A table file of chromosomes' size.
chr1 249250621
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chr8 146364022
chr9 141213431
chr10 135534747
(...)- The bowtie2 indexes. See the bowtie2 manual page for details about how to create such indexes.
- First have a look at the help message !
HiC-Pro --help
usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
Use option -h|--help for more information
HiC-Pro 2.7.0
---------------
OPTIONS
-i|--input INPUT : input data folder; Must contains a folder per sample with input files
-o|--output OUTPUT : output folder
-c|--conf CONFIG : configuration file for Hi-C processing
[-p|--parallel] : if specified run HiC-Pro in PBS/Torque mode
[-s|--step ANALYSIS_STEP] : run only a subset of the HiC-Pro workflow; if not specified the complete workflow is run
mapping: perform reads alignment
proc_hic: perform Hi-C filtering
quality_checks: run Hi-C quality control plots
build_contact_maps: build raw inter/intrachromosomal contact maps
ice_norm: run ICE normalization on contact maps
[-h|--help]: help
[-v|--version]: version- Copy and edit the configuration file 'config-hicpro.txt' in your local folder. See the
manual <MANUAL>for details about the configuration file - Put all input files in a rawdata folder. The input files have to be organized with a folder per sample.
- Run HiC-Pro
- On your laptop
MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_RAW_DATA -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE- Using a cluster (PBS)
MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_RAW_DATA -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE -pYou will get the following message :
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.shExecute the displayed command from the output folder:
qsub HiCPro_step1.sh
774410[].torque.curie.frThen wait for the torque mails... :) Once executed succesfully (may take several hours), then type:
qsub HiCPro_step2.shSmall fastq files (2M reads) extracted from the Dixon et al. 2012 paper are available for test.
## Get the data. Will download a test_data folder and a configuration file
wget -r -nH --cut-dirs=2 --no-parent --reject="index.html*" https://zerkalo.curie.fr/partage/HiC-Pro/
## Run HiC-Pro
time HICPRO_INSTALL_DIR/bin/HiC-Pro -i test_data -o HiC_Pro_v2.4.0_test -c config_test.txt
Run HiC-Pro
--------------------------------------------
lundi 2 mars 2015, 17:00:36 (UTC+0100)
Bowtie2 global alignment ...
bowtie_wrap.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt -u >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:01:25 (UTC+0100)
Bowtie2 local alignment ...
bowtie_wrap.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt -l >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:01:41 (UTC+0100)
Combine both alignment ...
bowtie_combine.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:01:52 (UTC+0100)
Bowtie2 mapping statistics for R1 and R2 tags ...
mapping_stat.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:01:53 (UTC+0100)
Pairing of R1 and R2 tags ...
bowtie_pairing.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:02:22 (UTC+0100)
Assign alignments to HindIII sites ...
mapped_2hic_fragments.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:03:49 (UTC+0100)
Merge multiple files from the same sample ...
merge_valid_interactions.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:03:49 (UTC+0100)
Make plots per sample ...
make_plots.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
--------------------------------------------
lundi 2 mars 2015, 17:03:55 (UTC+0100)
Generate binned matrix files ...
build_raw_maps.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt 2> logs/build_raw_maps.log
--------------------------------------------
lundi 2 mars 2015, 17:03:57 (UTC+0100)
Run ICE Normalization ...
normContactMaps.sh -c /bioinfo/users/nservant/projects_dev/HiC-Pro/config_test.txt >> hicpro_IRM90_rep1_split.log
real 3m23.902s
user 5m22.956s
sys 0m40.243s
## All results are available in HiC_Pro_v2.4.0_test
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