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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 https://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: [email protected] 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.
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A large scale off-target analysis tool for CRISPR/Cas9 genome editing system
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