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update doc
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‎LOGBOOK

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##
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################################################################################
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o Specify a chromosome subsets in the configuration file (to deal with random for instance)
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o It seems that recent PE data does not have the same read names ??
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o Look at issues about good practice installation

‎README.rst

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## Run HiC-Pro
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time HICPRO_INSTALL_DIR/bin/HiC-Pro -c config_test_latest.txt -i test_data -o hicpro_latest_test
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Run HiC-Pro 2.7.7
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Run HiC-Pro 2.10.0
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--------------------------------------------
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mercredi 15 juin 2016, 20:44:23 (UTC+0200)
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vendredi 22 décembre 2017, 13:34:18 (UTC+0100)
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Bowtie2 alignment step1 ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/bowtie_wrap.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt -u >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/bowtie_wrap.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt -u >> hicpro.log
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mercredi 15 juin 2016, 20:44:59 (UTC+0200)
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vendredi 22 décembre 2017, 13:34:55 (UTC+0100)
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Bowtie2 alignment step2 ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/bowtie_wrap.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt -l >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/bowtie_wrap.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt -l >> hicpro.log
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--------------------------------------------
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mercredi 15 juin 2016, 20:45:17 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:05 (UTC+0100)
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Combine both alignment ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/bowtie_combine.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/bowtie_combine.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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mercredi 15 juin 2016, 20:45:21 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:09 (UTC+0100)
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Bowtie2 mapping statistics for R1 and R2 tags ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/mapping_stat.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/mapping_stat.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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mercredi 15 juin 2016, 20:45:22 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:10 (UTC+0100)
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Pairing of R1 and R2 tags ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/bowtie_pairing.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/bowtie_pairing.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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mercredi 15 juin 2016, 20:45:30 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:16 (UTC+0100)
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Assign alignments to restriction fragments ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/mapped_2hic_fragments.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/mapped_2hic_fragments.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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mercredi 15 juin 2016, 20:46:08 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:45 (UTC+0100)
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Merge multiple files from the same sample ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/merge_valid_interactions.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/merge_valid_interactions.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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mercredi 15 juin 2016, 20:46:09 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:46 (UTC+0100)
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Merge stat files per sample ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/merge_stats.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/merge_stats.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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vendredi 22 décembre 2017, 13:35:46 (UTC+0100)
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Run quality checks for all samples ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/make_plots.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt -p "all" >> hicpro.log
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/make_plots.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt -p "all" >> hicpro.log
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mercredi 15 juin 2016, 20:46:22 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:55 (UTC+0100)
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Generate binned matrix files ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/build_raw_maps.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/build_raw_maps.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt
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mercredi 15 juin 2016, 20:46:23 (UTC+0200)
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vendredi 22 décembre 2017, 13:35:56 (UTC+0100)
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Run ICE Normalization ...
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/home/nservant/Apps/HiC-Pro_2.7.7/scripts/ice_norm.sh -c /home/nservant/projects_dev/HiC-Pro/config_test_latest.txt >> hicpro.log
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real 2m6.366s
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user 3m24.493s
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sys 0m33.151s
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/home/nservant/Apps/HiC-Pro_2.10.0/scripts/ice_norm.sh -c /home/nservant/Desktop/hicpro_dev/test-op/config_test_latest.txt >> hicpro.log
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real1m38.855s
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user3m13.344s
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sys0m31.432s
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Using HiC-Pro in a Singularity container
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========================================
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‎doc/ERRORS.rst

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Frequently Reported Errors
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Please see the HiC-Pro forum (https://groups.google.com/forum/#!forum/hic-pro) and the github issue page (https://github.com/nservant/HiC-Pro)
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HiC-Pro does not generate any maps
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‎doc/UTILS.rst

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4- hicpro2juicebox.sh
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or **How can I generate load my HiC-Pro data into Juicebox visualization software ?**
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or **How can I load my HiC-Pro data into Juicebox visualization software ?**
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| The hicpro2juicebox.sh utility allows to generate input file for Juicebox.
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| It can be use both for restriction fragment Hi-C or Dnase Hi-C by specifying the -f FRAGMENT_FILE option. Note that in this case, it is advice to use the HiC-Pro annotation file, as the fragment name is expected to be HiC_CHROMOSOME_FRAGMENTNUMBER.
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.. code-block:: bash
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## Convert HiC-Pro output to Juicebox input
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HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g hg19 -j /usr/local/juicebox/juicebox_clt_1.4.jar
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HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicebox/juicebox_clt_1.4.jar
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## Convert HiC-Pro output to Juicebox input up to restriction fragment resolution
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HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g hg19 -j /usr/local/juicebox/juicebox_clt_1.4.jar -f HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed
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HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicebox/juicebox_clt_1.4.jar -f HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed
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5- sparseToDense.py
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HICPRO_PATH/bin/utils/hicpro2fithic.py -i hic_results/matrix/dixon_2M/raw/1000000/dixon_2M_1000000.matrix -b hic_results/matrix/dixon_2M/raw/1000000/dixon_2M_1000000_abs.bed -s hic_results/matrix/dixon_2M/iced/1000000/dixon_2M_1000000_iced.matrix.biases
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6- hicpro2higlass.sh
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-------------------
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or **How can I load my HiC-Pro output into the Higlass visualization tool ?**
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| First be sure that Higlass is install on the environment and that the cooler python package is available.
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| See http://gehlenborglab.org/research/projects/higlass/ for higlass installation
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| See https://github.com/mirnylab/cooler for .cool Hi-C data format. The path to cooler utility must be defined in your PATH.
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.. code-block:: bash
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## Convert matrix file into .cool file
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HICPRO_PATH/bin/utils/hicpro2higlass.sh -i hic_results/matrix/dixon_2M/raw/1000000/dixon_2M_1000000.matrix -c chrom_hg19.sizes -n
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## Convert matrix file into .cool file
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HICPRO_PATH/bin/utils/hicpro2higlass.sh -i hic_results/data/dixon_2M/dixon_2M_allValidPairs -r 40000 -c chrom_hg19.sizes -n
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