mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-07 20:27:02 +01:00
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
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.
|
|
|
|
An R-function used for kinetic CRAC analysis can be found in
|
|
/usr/share/pyCRAC-$VERSION/kinetic_crac_pipeline
|
|
|
|
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:
|
|
|
|
The CRAC_pipeline_PE.py and CRAC_pipeline_SE.py scripts now ONLY work
|
|
with pyCRAC version 1.3.3 and Flexbar version 3.4.0 and later(!)
|
|
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.
|
|
|