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Contents of README:The pyCRAC package is a collection of python scripts to analyse high throughput data generated by RNA-sequencing, especially of molecules crosslinked by UV to an immunoprecipitated protein of interest (i.e. data generated by CLIP or CRAC protocols). It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. Included is the pipeline used for the analysis of a group of CRAC data sets. References Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8. PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Webb S, Hector RD, Kudla G, Granneman S. Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5 Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. van Nues R, Schweikert G, de Leau E, Selega A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S. If you want to run the test suite after installation, see README.tests. Note on the Crac pipelines: Use the -h flag to get a detailed help menu. The CRAC_pipeline_PE.py script needs to be run from the folder that contains the fastq files The barcode list file should contain two tab-separated columns in which the first column is the barcode sequence and the second column is the name of the experiment The file containing the adapter sequences should be in the fasta format. The chromosome_lengths file should contain two tab-separated columns in which the first column has the chromosome name and the second the chromosome length. |
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Parent Directory - README 04-Jun-2022 07:50 1.6K README.tests 04-Jun-2022 07:50 339 crac_pipelines-master.tar.gz 04-Jun-2022 07:51 29M pyCRAC-1.5.1.tar.gz 04-Jun-2022 07:50 18M pyCRAC.SlackBuild 11-Mar-2022 06:34 3.6K pyCRAC.info 04-Jun-2022 07:50 521 setup_slack.py 11-Mar-2022 06:34 3.4K slack-desc 04-Jun-2022 07:50 961 test_slack.sh 13-Apr-2019 02:03 9.7K
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