|Thread||Thread Starter||Forum||Replies||Last Post|
|Find out SNPs and Mutations in RNA-Seq data||suz.katie||Bioinformatics||0||12-14-2012 10:01 AM|
|Can VarScan be used to find out Somatic Mutations in RNA seq Data ?||swapnil2188||RNA Sequencing||1||12-10-2012 08:13 AM|
|Bis-SNP: An accurate SNP and methylation calling tool for Bisulfite-Seq/NOMe-seq/RRBS||DNAase||Bioinformatics||4||10-29-2012 03:53 PM|
|Tools or ways to find out variants in RNA seq data ?????||swapnil2188||RNA Sequencing||4||02-06-2012 01:03 PM|
|How to find coverage for RNA-seq, solid data?||pinki999||Bioinformatics||2||09-28-2011 05:59 AM|
|04-03-2013, 05:33 PM||#1|
Location: Purdue University
Join Date: Nov 2009
Cannot find NOME-Seq data
I am trying to find some NOME-Seq data, but I cannot locate it.
Here is the study ...
Genome Research 2012
"Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules"
Theresa K. Kelly, Yaping Liu, Fides D. Lay, Gangning Liang, Benjamin P. Berman, and Peter A. Jones
Here is the information about Data Access ...
NOMe-seq tracks for genomic viewers (Fig. 2; Supplemental Fig. S2)
are available as a supplemental document and at http://epigenome.
usc.edu and the NCBI Gene Expression Omnibus (GEO) (http://
www.ncbi.nlm.nih.gov/geo/) under accession number GSE21823.
All source code tools are available at http://sourceforge.net/projects/
uecgatk/. See Supplemental Material for instructions on using these
tools. The tool and source code for the new module of the IGV
viewer to display NOMe-seq data from raw BAMalignment files are
publicly available for download at the IGV project website, http://
I can only find MNase-Seq data at GEO. I can't find publically available BAM files either. I just want a processed file with coordinates and fractions of methylated GpCs and CpGs to infer occupancy and % CpG methylation.
|04-03-2013, 07:00 PM||#2|
Location: Sydney, Australia
Join Date: Jun 2011
When you click on a GSE record, there is a contact e-mail for the person who created the record. You should ask him.
|04-04-2013, 09:13 AM||#3|
Location: Los Angeles
Join Date: Dec 2009
Here is the GEO file for that paper:
feel free to contact me
USC Epigenome Center