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27 lines
1.1 KiB
Text
27 lines
1.1 KiB
Text
The pyCRAC package is a collection of python2-scripts to analyse high
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throughput data generated by RNA-sequencing, especially of molecules
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crosslinked by UV to an immunoprecipitated protein of interest (i.e.
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data generated by CLIP or CRAC protocols).
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It can be used to remove duplicate reads,tackles directional libraries
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and reports sense and anti-sense hits.
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Included is the pipeline used for the analysis of a group of CRAC data
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sets.
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An R-function used for kinetic CRAC analysis can be found in
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/usr/share/pyCRAC/kinetic_crac_pipeline
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References
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Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8.
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PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription
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termination regulates expression of hundreds of protein coding genes in
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yeast. Webb S, Hector RD, Kudla G, Granneman S.
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Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5
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Kinetic CRAC uncovers a role for Nab3 in determining gene expression
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profiles during stress. van Nues R, Schweikert G, de Leau E, Selega
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A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G,
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Granneman S.
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If you want to run the test suite after installation, see README.tests.
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