##Get Started
$ git clone --depth=1 https://github.com/r3fang/Hicmap_Ren.git
$ cd Hicmap_Ren
$ bash install.sh
$ # download demo HiC data
$ wget http://enhancer.sdsc.edu/r3fang/Hicmap_Ren/demo_R1.fastq.bz2
$ wget http://enhancer.sdsc.edu/r3fang/Hicmap_Ren/demo_R2.fastq.bz2
$ wget http://enhancer.sdsc.edu/r3fang/Hicmap_Ren/cutter_sites.tar.gz
$ tar -xvzf cutter_sites.tar.gz
$ mkdir BWAIndex/; wget http://enhancer.sdsc.edu/r3fang/Hicmap_Ren/mm9.fa -P BWAIndex
$ bwa index BWAIndex/mm9.fa
$ hicmap -f demo_R1.fastq.bz2 -r demo_R2.fastq.bz2 -n demo -p Picard/MarkDuplicates.jar \
-g BWAIndex/mm9.fa -c cutter_sites/mm9.Hind3.1000bp.bed
##Depedency
##Introduction
Hicmap is a fast pipeline for mapping Hi-C data.
$ hicmap
Program: hicmap (Hi-C analysis pipeline)
Version: v07.04.2016
Contact: Rongxin Fang <[email protected]>
Lab: http://bioinformatics-renlab.ucsd.edu/rentrac/
usage: hicmap [-h] [-t THREADS] [-m MAX_MEM] [-f FASTQ1] [-r FASTQ2] [-p MarkDuplicates.jar] [-n PREFIX] [-g BWA_GENOME] [-c CUT_SITES] [-i INSERT_SIZE]
Example:
hicmap -f demo_R1.fastq.bz2 -r demo_R2.fastq.bz2 -p Picard/MarkDuplicates.jar -n demo -g genome.fa -c mm9.MboI.bed
Options:
-- required:
-f FASTQ1 first mate of pair-end sequencing data [.fq|.gz|.bz2].
-r FASTQ2 second mate of pair-end sequencing data [.fq|.gz|.bz2].
-p MARK_DUPLICATE path to picard MarkDuplicates.jar [Picard/MarkDuplicates.jar].
-n NAME prefix of output files.
-g BWA_GENOME BWA indexed reference genome.
-c CUT_ENZ restriction cutter sites files.
-- optional:
-i INSERT_SIZE pairs with distance smaller that MIN_INSERT_SIZE will be filtered [10,000].
-t INT threads to be used for BWA mapping [2].
-m MAX_MEM max memory will be used for .bam sorting and MarkDuplicates.jar [2G].
##Version
v07.04.2016
##Author
Rongxin Fang
[email protected]
hicmap_ren's People
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