This is the Linux app named CIMS whose latest release can be downloaded as CIMS.v1.0.5.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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CIMS
DESCRIPTION
This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data.
References:
Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293.
Zhang,C.†, Darnell, R.B.†2011. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotech. 29:607-614.
Features
- Mapping raw CLIP reads to the reference genome (using novoalign)
- Collapsing PCR duplicates with different models depending on presence of random barcodes
- Cluster CLIP tags to identify clusters and determine peak heights
- Tracking mutations (insertions, deletions and substitutions) in unique CLIP tags
- Identifying robust cross linking induced mutation sites (CIMS)
- Identifying robust cross linking induced truncation sites (CITS) from BrdU-CLIP, iCLIP or other similar variations
Audience
Advanced End Users
User interface
Command-line
Programming Language
Perl
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/ngs-cims/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
