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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
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Bio-InformaticsLicense
GNU General Public License version 3.0 (GPLv3)Follow CIMS
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