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Command line tool for crispr offtarget finding extracted from crispor website

Project description

# CRISPOR - a CRISPR/Cas9 assistant

CRISPOR predicts off-targets in the genome, ranks guides, highlights
problematic guides, designs primers and helps with cloning. Try it on

CRISPOR uses BWA, a few tools from the UCSC Genome Browser (twoBitToFa, bedClip),
various R packages and a huge collection of external packages and source code files
from published articles, see the file for the exact references.

Installation of the package:

make crispor_env

source crispor_env/bin/activate

make devbuild

Install required R libraries:

sudo Rscript -e 'install.packages(c("e1071"), repos="")'
sudo Rscript -e 'source(""); biocLite(c("limma"));'

Now in a python console type this:

from crispor_cli import crispor


Description for args and options is given below:
Here args is a list containing org,fastaInFile and guideOutFile in this order:
Example args -

And options is a dictionary containing all the extra options permitted by crispor.
Example options -
options = {'offtargetFname':'/output/yo_off.tsv','pam':'NGG','debug':True,'skipAlign':True}

Here are the keys that can be added to options dictionary-

debug - show debug messages, do not delete temp directory
test - run internal tests
pam - PAM-motif to use, default NGG. TTTN triggers special
Cpf1 behavior: no scores anymore + the PAM is assumed
to be 5' of the guide. Common PAMs are:
offtargetFname -
write offtarget info to this filename
maxOcc -
MAXOCC parameter, guides with more matches are

maximum number of mismatches, default 4

skipAlign -
do not align the input sequence. The on-target will be
a random match with 0 mismatches.
noEffScores -
do not calculate the efficiency scores
minAltPamScore -
minimum MIT off-target score for alternative PAMs, default
directory with genomes, default ./genomes

# Licenses

Included software:

* BWA is under GPL3
* libSVM: under copyright by Chih-Chung Chang and Chih-Jen Lin see
* svmlight: free for non-commercial use, see
* SSC: no license specified
* primer3: GPL2.
* Fusi/Doench score: see LICENSE.txt, (c) by Microsoft Research
* and themselves are released under GPLv3, see LICENSE.txt

Project details

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