This repo has migrated to crisprReadCountsPy.

crisprReadCounts

Gets CRISPR read counts from cram files and merges readcounts from multiple read count files.

Master	Dev

Dependencies/Install

Please use setup.sh to install minor dependancies (perl libraries).

./setup.sh /some/install/location

Usage

crisprReadCounts.pl [-h] -i /your/input/file.cram -l /your/library/file -p /plasmid/readcount/file -o output_file

crisprMergeResults.pl [-h] -o /your/output/file -i file1,file2,file3,file4 -p y

crisprDualGuideCounts.pl [--help] --sample sample_name --library library_file --fastq1 R1_fastq --fastq2 R2_fastq --reads reads.tsv --stats stats.tsv --counts counts.tsv

Options

Please see the help generated by crisprReadCounts.pl or crisprMergeResults.pl when executed with no parameters for up-to-date information.

Creating a release

Preparation

Commit/push all relevant changes.
Pull a clean version of the repo and use this for the following steps.

Cutting the release

Update lib/Sanger/CGP/crispr.pm to the correct version.
Update CHANGES.md to show major items.
Check all tests and coverage reports are acceptable.
Commit the updated docs tree and updated module/version.
Push commits.
Use the GitHub tools to draft a release.

Docker container

crisprReadCounts is available as a Docker container on Quay.io.

LICENCE

Author: CASM/Cancer IT cgphelp@sanger.ac.uk

This file is part of crisprReadCounts.

crisprReadCounts is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."

cancerit/crisprReadCounts