Bismark: bismark2bedGraph option to add trinucleotide context option · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Bismark: bismark2bedGraph option to add trinucleotide context option

Hi everybody, I just started to use Bismark and I love it. However I missing one option to add the trinucleotide context of cytosines which I analyse. Since Iam interested in both CpG as well as non CpG methylation this information would be great. I know "coverage 2cytosine" has this additional information but since Iam only interested in very small regions of the genome (BSamplicon-seq) it would be a wast of resources to use this module.

May someone has a idea ?

Thanks a lot, Flo

bisulfite-sequencing dna methylation bismark

• 2,332 views • link

written 10.1 years ago by florian.noack •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Generating 5mCG or 5hmCG values per gene from BS/OXBS data
written 4.3 years ago by hchetia •

Hi, I use the methread function to read the coverage files from Bismark. ``BS_21=methRead("2368_bismark_bt2_pe.deduplicated.bismark.cov.gz", sample.id="2368_BS",assembly="mm10", header=F,skip=0,sep="\t",context="CpG", pipeline="bismarkCoverage", mincov = 5) However, the resulting methylkit object …
Difference in Bismark output methylation call files and coverage files
written 6.1 years ago by linelr •

Hi biostars! I am working with RRBS data and have used Bismark for methylation calls. I have compared the two output files with cytosines in …
Anyone have experience with crossing methylation markers (CpGs) with SNPs?
written 7.1 years ago by spela.salamon •

I would like to take a series of methylation markers (CpGs) and match them to a set of GWA SNPs. I have been trying to …
Some questions for the 'readTranscriptFeatures' function of the R package-"genomation" when I doing…
written 7.4 years ago by ying.senhong •

Hello, When I was doing the RRBS analysis, I used bismark+methylKit. After find DMR, I try to annotation these DMRs. But when I using the …
Bismark Methyl-Seq Analysis
written 9.1 years ago by Seq225

We have sequenced a genome using Illumina's True-seq bisulfite sequencing kit. After getting back the seq, we are analyzing methylation rate using Bismark. I Need …
Bisulfite Sequencing-Bismark: Observing abnormally high methylation levels
written 9.3 years ago by ryanzapotocny •

I am using currently using Bismark to align bisulfite-treated reads to the soybean genome. After running the methylation_extractor script on some of my samples it …
Tool to compare whole genebody enrichment between different samples (MeDip-seq)
written 10.3 years ago by florian.noack •

Hi everyone, I have some MeDip datasets and did already comparisions of my datasets based on peaksets (MACS2). However I would like to find out …
Comparison of two MeDip data sets
written 10.5 years ago by florian.noack •

Hi everybody, I have (h)MeDip data from two different cell types I would like to compare to identify D(h)MR between the two cells. I used …
how to get all gc/cpg positions in the latest human genome (gencode hg19)
written 12.1 years ago by Saad Khan

Hi, I am trying to reuse some publicly available results of bisulfite methylation analysis. These contain mc tables which do not have strand information. The …
Dna Methylation Of Cpg Sites Near Gene Of Interest
written 12.7 years ago by qliu2011 •

<p>Do we currently have any information (research studies, models, ...etc) on how far away a CpG site is from a specific gene of interest where …