hicpro分步走

ref1：github: https://github.com/nservant/HiC-Pro

ref2: 说明书：http://nservant.github.io/HiC-Pro/

ref3：谷歌论坛：https://groups.google.com/forum/?nomobile=true#!forum/hic-pro

完整：

HiC-Pro -i test_data -o hicpro_output -c config.txt

step1：mapping：

HiC-Pro -i test_data -o hicpro_output -c config.txt -s mapping

生成：hicpro_output/bowtie_results/bwt2/dixon_2M/ {bwt2 bwt2_global bwt2_local}

step2：proc_hic

HiC-Pro -i hicpro_output/bowtie_results/bwt2/ -o hicpro_output/ -c config.txt -s proc_hic

生成：hicpro_output/hic_results/data/dixon_2M（各种pairs文件）

要求：只要在目录下有R1/R2两个比对好的bam文件即可

step3：quality_checks

HiC-Pro -i hicpro_output/hic_results/data/ -o hicpro_output/ -c config.txt -s quality_checks

生成： hicpro_output/hic_results/pic/dixon_2M/xxx.pdf

step4：build_contact_maps

cp hicpro_output/hic_results/data/dixon_2M/SRR400264_00_GRCh37.bwt2pairs.validPairs hicpro_output/hic_results/data/dixon_2M/SRR400264.allValidPairs

因为需要有XXX.allValidPairs

HiC-Pro -i hicpro_output/hic_results/data/ -o hicpro_output/ -c config.txt -s build_contact_maps

生成：hicpro_output/hic_results/matrix/dixon_2M/raw/50000/XXX.matrix

step5：ice_norm

HiC-Pro -i hicpro_output/hic_results/matrix/ -o hicpro_output/ -c config.txt -s ice_norm

生成：hicpro_output/ice_norm/hic_results/matrix/dixon_2M/iced/50000/XXX.matrix