HiCAT

Tool for Hi-C data analysis.

Software Requirements

Bowtie: the latest version of BWA should be installed from http://bowtie-bio.sourceforge.net Shell: awk python 2.7

Usage

     -1              The input R1 fastq or fastq.gz files. Files seperated by comma.
     -2              The input R2 fastq or fastq.gz files. Files seperated by comma.
                     The order of files can paired with R1 files.
     -o              The output dir.'
     --label         The lable for each paired R1_R2 fastq files, seperated by comma.
     -g              The bowtie index.
     -p              Cpus. Default:1.
     -n              The mismatch number for bowtie mapping. Default=2.
     -5              Trim bases number of 5 prime.
     -3              Trim bases number of 3 prime.
     --re            The resites for cut unmapped fastq files. It is the cut site from 5'-> 3'.
                     Default, DPNII:GATC.'
    --genomic_dis   The length for remove genomic DNA.Default:500.
    --start_search_REsite       The starting step is search REsite.If set, you should set old_file_dir.
    --start_REsite_mapping      The starting step is search RE reads mapping.If set, you should set old_file_dir.
    --old_file_dir              If not start at the full length map step,set this to get former files.
    --keep_media_fq_files       If set, keep the median sam and fastq files. Default delete them.

Run

HiCAT.py -1  A.R1.fastq,B.R1.fastq  -2  A.R2.fastq,B.R2.fastq  -o  out  --label A,B  -g  bowtie_index -p 10 -n 2 --re GATC