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.

pyCrac uses alignmemnt files (.sam, .bam or .novo) as input for the
pyReadAligner.py and pyPileup.py functions. Novoalign (for .novo 
files) is no longer available without a paid license.


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.