cims

We have hosted the application cims in order to run this application in our online workstations with Wine or directly.

Quick description about cims:

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: