Download

Source code for command line use is available at bitbucket.org

Introduction

The source is the command line version of this website, while it can do the following extra things,

  • can do scan for other species if the assembly nib and bwa index file is given
  • no sequence length limit.
  • Install

    Requirement

  • 2.6 <= Python < 3
  • bx-python
  • tabix
  • SSC
  • Get the source code

    hg clone https://bitbucket.org/jianma/crisprdo
    Go to the crisprdo directory and type this to install for all users:
    sudo python setup.py install
    Or use this command to install for only you:
    python setup.py install --user
    If you install locally, you may need to add the location to your $PATH and $PYTHONPATH. These two lines can be added to .bashrc file so it will load each time you login.
    export PYTHONPATH=${HOME}/.local/lib/python2.7/site-packages:${PYTHONPATH}
            export PATH=${HOME}/.local/bin:${PATH}
        
    and run
    crispr-do

    Usage

        Usage: crispr-do <-g genome -c chrX --start=START --end=END> [options]
    
        sgRNA design for a region.
    
        Options:
          --version             show program's version number and exit
          -h, --help            Show this help message and exit.
          -g GENOME             Genome assembly version
          -c CHROM, --chrom=CHROM
                                chromosome, e.g.chr1
          --start=START         start site of the region
          --end=END             end site of the region
          --annotation          If to annotation the sgRNAs with DHS, SNP or exons.
                                default (not set): False
          --lasso-cutoff=LASSO_CUTOFF
                                lasso_cutoff
          --job-id=JOB_ID       any string or hash code to identify this run
        

    The nib file and bwa index is necessary for run the spacers scan. To scan spacers in a region without do annotation, try this

     crispr-do -g GENOME -c CHROM --start=START --end=END --job-is=NAME

    To do annotation, you need extra static files, DHS, SNP and exon files.

    Output

    The output is called "spacer" in the directory of your JOB_ID. Here's the meaning of each column of that file

    chromthe chromosome name the sgRNA located.
    startstart position of the sgRNA in genome
    endend position of the sgRNA in genome
    hitseqsgRNA sequence, containing the PAM (in red) and 7bp downstream.
    strandon which strand the sgRNA located
    efficiency_scorethe efficiency of the sgRNA based on its 30bp sequcene.
    specificity_scorethe specificity of the sgRNA. This score is ranged from 0 to 100
    conservation_scoreaverage conservation score in 30bp sequence (20bp guide + PAM + 7bp), using UCSC phastcons score

    and extra 3 columns with annotation option.

    DHS_overlapif the sgRNA is overlapped with any DHS regions from encode
    SNP overlapif there are any SNP located in the sgRNA
    exon_overlapif the sgRNA is overlapped with any exon

    Static data download

    genome nib files
    hg19 hg38 mm9 mm10 danRer7 dm6 ce10

    genome chromosome length
    download

    bwa index
    The bwa index is not available for download, you can build it with official BWA scripts.

    DHS
    hg19 hg19_index
    hg38 hg38_index
    mm9 mm9_index
    mm10 mm10_index
    not available for danRer7, dm6 and ce10

    SNP
    hg19 hg19_index
    hg38 hg38_index
    mm9 mm9_index
    mm10 mm10_index
    danRer7 danRer7_index
    dm6 dm6_index
    ce10 ce10_index

    exon
    hg19 hg19_index
    hg38 hg38_index
    mm9 mm9_index
    mm10 mm10_index
    danRer7 danRer7_index
    dm6 dm6_index
    ce10 ce10_index