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Exome-based analysis for RNA epigenome sequencing data.

ABSTRACT:

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/.

SUBMITTER: Meng J

PROVIDER: S-EPMC3673212 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Exome-based analysis for RNA epigenome sequencing data.

Meng Jia J Cui Xiaodong X Rao Manjeet K MK Chen Yidong Y Huang Yufei Y

Bioinformatics (Oxford, England) 20130414 12

<h4>Motivation</h4>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.<h4>Result</h4>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 acco ...[more]

PMID: 23589649

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