/crisprReadCounts

Code to do read counts for CRISPR data

Primary LanguagePerlGNU Affero General Public License v3.0AGPL-3.0

This repo has migrated to crisprReadCountsPy.


crisprReadCounts

crisprReadCounts

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

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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

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

Docker container

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


LICENCE

Copyright (c) 2014-2019 Genome Research Ltd.

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/.

  1. 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’."