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CIMS download for Linux

Free download CIMS Linux app to run online in Ubuntu online, Fedora online or Debian online

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

Bio-Informatics

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.


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