README

ABOUT
         offscan.pl - A perl script used for large scale profiling possible
                      target sites of CRISPR/CAS9 system by using seqmap

VERSION
         Version: 1.5.1
         Jul 24, 2017

SYNOPSIS
         $ perl ./offscan.pl <option>
         For usage, type './offscan.pl -h'
         To test a demo, type './offscan.pl -t'

DESCRIPTION
         This script takes a FASTA file of the target sites and queries the
         reference database by seqmap tolerant designated mismatches, and gives
         the human readable and computer mineable target/off target sites and
         flanking sequencing, also the summary file.

         Seqmap is describled:
         Jiang, H. and Wong, WH. (2008) SeqMap: mapping aassive amount of
         oligonucleotides to the genome, Bioinformatics, 24(20):2395-2396.
         And available at http://www-personal.umich.edu/~jianghui/seqmap/

         This script is firstly used in the following research:
         Guo, XG., Zhang, TJ., Hu, Z., Zhang, YQ., Shi ZY., Wang, QH., Cui, Y.,
         Wang, FQ., Zhao, H. and Chen, YL. (2014) Efficient RNA/Cas9-mediated
         genome editing in Xenopus tropicalis. Development, 141(3):707-714.

NOTE
         1. Max number of mismatch (option -n) is 5.
         2. The type memory size (option -m) is a number. Unit: megabyte.
         3. User can download the latest seqmap and replace the one included in
            directory 'bin'.

AUTHOR
         Wang, Qinhu
         Northwest A&F University
         E-mail: wangqinhu@nwafu.edu.cn

LICENSE
         For non-commercial use only.
		 


cas9off version 1.5.1
=====================

Usage:

    offscan.pl <option>

    -h  Help
    -t  Test demo
    -g  Query RNA file, in sgRNA desinger output format
    -q  Query RNA file, in FASTA format
    -r  Query RNA length, default is 23 bp, including NGG
    -d  Database file, in FASTA format, contains reference sequences
    -l  Length of flanking sequences to extract, default is 500 bp
    -n  Number of mismatch (0-5), does not include NGG
    -o  Output filename, default is cas9off.xls
    -s  Summary filename, default is sum.xls
    -m  Memory size, default is 2048 [Mb (2Gb)]
    -f  Format reference sequence or not, can be 'true' [default] or 'false',
        critical if your FASTA file has annotation
    -a  Path of seqmap
    -b  Map file, seqmap output

    For citation:
	
    * Jiang, H. and Wong, WH. (2008) SeqMap: mapping aassive amount of 
      oligonucleotides to the genome, Bioinformatics, 24(20):2395-2396.
	
    * Guo, XG., Zhang, TJ., Hu, Z., Zhang, YQ., Shi ZY., Wang, QH., Cui, Y.,
      Wang, FQ., Zhao, H. and Chen, YL. (2014) Efficient RNA/Cas9-mediated
      genome editing in Xenopus tropicalis. Development, 141(3):707-714.