Let’s defined a few variables
HiC-Pro -i ${TEST_DATA} -o ${RES_PREFIX}_1 -c config_test.txt
HiC-Pro -i ${TEST_DATA} -o ${RES_PREFIX}_2 -c config_test.txt -p
cd ${TEST_DATA}
qsub HiCPro_step1_test.sh
## wait ...
qsub HiCPro_step2_test.sh
I first want to align to raw reads and make the quality controls on the mapping results using the parallel mode
HiC-Pro -i ${TEST_DATA} -o ${RES_PREFIX}_3 -c config_test.txt -s mapping -s quality_checks -p
cd ${RES_PREFIX}_3
qsub HiCPro_step1_mappingtest.sh
Once the reads are mapped, let’s run the Hi-C processing step from the aligned data on my own laptop
HiC-Pro -i ${RES_PREFIX}_3/bowtie_results/bwt2 -o ${RES_PREFIX}_3.1 -c config_test.txt -s proc_hic -s quality_checks
Everything looks good, I can then create the contact maps and normalize them
HiC-Pro -i ${RES_PREFIX}_3.1/hic_results/data -o ${RES_PREFIX}_3.2 -c config_test.txt -s build_contact_maps -s ice_norm
First set the ALLELE_SPECIFIC_SNP variable in the configuration file and check whether the N-masked genome is available. Then simply run HiC-Pro as usually. See the allele specific section for details.
HiC-Pro -i ${TEST_DATA} -o ${RES_PREFIX}_5 -c config_test_as.txt
HiC-Pro is able to process Hi-C data generated without restriction enzyme, such as DNase Hi-C. To analyse such data, simply unset the variable LIGATION_SITE and GENOME_FRAGMENT from the configuration file. As the ligation site is unknown, the mapping will be done in only one step (step 2 is not run). Then, the uniquely mapped reads are directly used to build the contact maps. In the context of DNase Hi-C, one way to filter out artefacts such as self ligation is to discard intra-chromosomal pairs below a given distance threshold. A filtering of the short contact distance is therefore proposed using the parameter MIN_CIS_DIST.
In practice, the processing of capture-C data has many common steps with standard Hi-C analyis. HiC-Pro can therefore be used for capture-C data until the detection of valid 3C products. You should therefore used HiC-Pro is stepwise mode with option “-s mapping -s proc_hic -s quality_checks -s merge_persample”. One the list of valid pairs available, we proposed an additional utility ‘make_viewpoints.py’ which is able to build bedgraph file for a given list of viewpoints.
HiC-Pro can also be used to process capture Hi-C data. In this case, you have to provide a BED file with the target regions and to set the variable CAPTURE_TARGET in the config file. After mapping and filtering, the valid pairs will be restricted to the intra-chromosomal interactions that occur within the designed regions. All other interaction will be removed. The interaction maps will therefore be build on that region.