Go Back   SEQanswers > Applications Forums > Epigenetics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to processing ENCODE small RNA-seq data dzmtnvmt Bioinformatics 4 05-14-2013 07:23 AM
Some queries on DNA methylation when processing the BS-seq data zeam Epigenetics 4 03-17-2011 08:40 AM
processing 454 rna-seq data acpatel RNA Sequencing 0 06-29-2009 11:26 AM

Thread Tools
Old 08-18-2013, 04:45 AM   #1
Location: boston

Join Date: May 2012
Posts: 29
Default MeRIPseq and m6A-seq data processing

If anyone is interested in RNA epigenetics or Post-transcriptional RNA modifications, we recently developed an R-package "exomePeak" for analysis of RNA epigenome sequencing data from MeRIPseq or m6A-seq.

The salient features of exomePeak R-package includes:
  • exome-based peak detection, suitable for RNA epigenetic regulation analysis
  • Statistically supports biological replicates, and reports consistent peaks which must appear on all biological replicates
  • Internally removes PCR artifacts and multimapping reads, so pre-processing is no longer necessary
  • The binding sites are reported in bed formats, which is compatible with most genome browser for easy visualization and manipulation
  • Comparison of two experimental conditions to unveil the dynamics in RNA epigenetic regulations

The exomePeak R-package depends on the Rsamtools R-package, and can be installed easily from internet with the following R commands:
# Install Rsamtools and exomePeak package
target=paste(web, file, sep="/")
download.file(target, destfile="exomePeak_1.0.tar.gz")
install.packages('exomePeak_1.0.tar.gz', repos = NULL, type = "source")
The package is still under active development and we welcome any suggestions and questions that make it more usable. We are also looking for potential collaboration opportunities. Please free to send me a message if you have any questions.

And the newly opened google group:

Jia Meng, PhD

Last edited by sqcrft; 08-18-2013 at 03:06 PM.
sqcrft is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:47 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO