slackbuilds-current/academic/pyCRAC/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.

A pipeline that streamlines the analysis of a group of CRAC datasets 
is available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines and
depends on the python package 'ruffus', also at slackbuilds.org. 



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.