MeRIPseq and m6A-seq data processing

sqcrft · 08-18-2013, 04:45 AM

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:

Code:

# Install Rsamtools and exomePeak package
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
web="http://www.broadinstitute.org/~jmeng/picower/PERMANENT"
file="RexomePeak/exomePeak_1.0.tar.gz"
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: https://groups.google.com/d/forum/rn...a-modification

Regards,
Jia Meng, PhD
jia.meng@mit.edu

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08-18-2013, 04:45 AM	#1
sqcrft Member Location: boston Join Date: May 2012 Posts: 29	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: Code: # Install Rsamtools and exomePeak package source("http://bioconductor.org/biocLite.R") biocLite("Rsamtools") web="http://www.broadinstitute.org/~jmeng/picower/PERMANENT" file="RexomePeak/exomePeak_1.0.tar.gz" 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: https://groups.google.com/d/forum/rn...a-modification Regards, Jia Meng, PhD jia.meng@mit.edu Last edited by sqcrft; 08-18-2013 at 03:06 PM.