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Diffstat (limited to 'academic/pyCRAC/README')
| -rw-r--r-- | academic/pyCRAC/README | 24 |
1 files changed, 22 insertions, 2 deletions
diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index a5be782d73..1583f3e62c 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -1,4 +1,4 @@ -The pyCRAC package is a collection of python2-scripts to analyse high +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). @@ -9,7 +9,7 @@ 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/kinetic_crac_pipeline +/usr/share/pyCRAC-$VERSION/kinetic_crac_pipeline References @@ -25,3 +25,23 @@ 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. + |