Saturday, June 8, 2013

Fwd: Exome-based analysis for RNA epigenome sequencing data

Fwd: please follow footer link

Exome-based analysis for RNA epigenome sequencing data: "

Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.

Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.

Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/.

Contact:yufei.huang@utsa.edu or jmeng@mit.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

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(Via Bioinformatics - current issue.)