[Bio-Linux] beta testers for pyCRAC, a set of user-friendly python tools for CLIP/CRAC data analyses

[Sander Granneman]

Hi All,

The CLIP and related CRAC techniques allow researchers to identify direct protein-RNA interactions in vivo and can be used in combination with high-throughput sequencing to get a comprehensive map of protein-RNA interactions transcriptome-wide. CLIP/CRAC data differ in many respects from data generated by transcriptome analysis or genome resequencing. These data analyses involved development of many new algorithms to extract all the relevant information and generation of new data processing pipelines. Many laboratories have expressed an interest in using the technique but were deterred by their lack of experience in tackling the CLIP/CRAC high-throughput datasets.

I am in the process of developing a python framework tailored to tackle CLIP/CRAC datasets and other directional RNAseq data. Using this foundation I have written a number of user-friendly (and hopefully intuitive) tools for the analysis of CRAC/CLIP datasets, including tools for motif searches on clusters, filtering reads based on the presence of mutations, generating pileups and multiple sequence alignments, tools for making genome browser compatible files, etc etc. The package also contains several modules (GTF2 parser, SAM/Novoalign single and paired-end parsers) which could be used for the rapid development of new scripts.

All the tools have detailed help menus and I have written an draft manual. 

I am looking for people who would be interested in testing these tools and I'm keen for some feedback. 

If you are interested in testing the package, please drop me an e-mail!

Sander

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Sander Granneman, PhD
Wellcome Trust RCD Fellow
Institute for Structural and Molecular Biology
Centre for Systems Biology at Edinburgh (CSBE)
Room 3.06, CH Waddington Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JD

Phone:
office: +44 (0) 131 651 9082
lab:	+44 (0) 131 651 9055

sgrannem at staffmail.ed.ac.uk

http://sandergranneman.bio.ed.ac.uk
http://www.csbe.ed.ac.uk/
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