Welcome to HiC-Pro’s documentation!
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Contents:
HiC-Pro Quick Start Guide
What is HiC-Pro ?
How to install it ?
Annotation Files
How to use it ?
Test Dataset
HiC-Pro Manual
Setting the configuration file
Run HiC-Pro in sequential mode
How does HiC-Pro work ?
Browsing the results
Allele specific analysis
Allele specific mapping
Assignment to parental genome
Allele specific maps
HiC-Pro Results
Mapping results
List of valid interaction products
Intra and inter-chromosomal contact maps
HiC-Pro Utilities
1- split_reads.py
2- extract_snps.py
3- digest_genome.py
4- make_viewpoints.py
4- hicpro2juicebox.sh
5- sparseToDense.py
6- hicpro2fithic.py
User cases
One mode for one environment
Supported protocols
COMPATIBILITY WITH OTHER SOFTWARE
Juicebox visualization software
HiCPlotter visualition software
TADs calling (Directionality Index)
Fit-Hi-C
R and HiTC BioConductor package
FAQ
HiC-Pro failed. How to find what’s going wrong ?
How can I split my .fastq files into smaller files ?
How can I used my own annotations files
How can I generate my annotation files ?
Why HiC-Pro need to be run in two steps in parallel mode ?
Does HiC-Pro support other mappers ?
How can I create N-masked genome for allele-specific analysis ?
What can I do once I have the iced contact maps
How can I visualize the maps generated by HiC-Pro
How much disk space is require for running HiC-Pro
Frequently Reported Errors
HiC-Pro does not generate any maps
Error - sort: stray character in field spec: invalid field specification `2,2V’
Error - pysam: AttributeError: ‘module’ object has no attribute ‘AlignmentFile’
Error in Paring of R1 and R2 tags