Tag: RRBS

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Installation Trim Galore is a a Perl wrapper around two tools: Cutadapt and FastQC. To use, ensure that these two pieces of software are available…

“Normal” percent duplication for RRBS reads? 1 Hi all, I recently have been working on a reduced representation bisulfite sequencing project (RRBS) where I was required to do 15-18 cycles of PCR to get libraries to a sufficient concentration for sequencing. Because of this, I ended up with quite a…

RnBeads Stuck in “STARTED Methylation Value Distributions – Sample Groups” 0 I am trying to run RRBS data on RnBeads, but it gets stuck at “STARTED Methylation Value Distributions – Sample Groups.” I am running Bismark outputs – bismark.cov, and my sample annotation header looks like this. Sample_ID description filename_bismark.cov…

Hello, I am trying to analyze data for RRBS (reduced representation bisulfite sequencing) and want to use BWA-METH for alignment. I also ran Bismark, but bismark output only shows mapping efficiency of 33.8% while BWA-METH shows 99.8% mapping efficiency (paired-end). So, I converted .sam to .bam with samtools and tried…

Hello, I want to use HMST-Seq anayzer (www.sciencedirect.com/science/article/pii/S2001037020304232) tool for my RRBS data analysis (directional) but I am stuck at the first step. In order to run HMST-Seq analyzer pipeline, I need CpG.txt or CpG.bed file as an input. So, I first performed bismark analysis on my control and mutated…

Position Description: Every great life-changing discovery begins the same way—with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do at the Medical College of Wisconsin….

Hi everyone, I’m currently looking at different software for RRBS analysis. My lab typically used rnbeads and I’m finding it difficult to find comparisons between it and other software such as bs-seeker3. I’ve seen comparisons of other tools but not rnbeads, am I comparing unrelated software? Back to the main…

Job Description Diagenode (a Hologic company) is an international biotech company that develops and commercializes innovative instruments and reagents systems for the life science research and molecular diagnostics. Founded in 2003, the Group is headquartered in Liège (Belgium), with subsidiaries in Denville (NJ, USA), in Toyama (Japan) and in Santiago…

Difference in Bismark output methylation call files and coverage files 1 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 a CpG-context and the coverage files (which only consider cytosines in a CpG context),…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

RRBS data analysis using Bismark and methylkit 0 Once we have read in the cytosine report files with methRead(), how to generate a table/dataframe of beta values or equivalent for all samples as columns and CpG sites as rows? Is the percMethylation() function the correct function to use? Beta values…

Bismark rrbs data analysis 1 Hello! I’m quite new in methyl-seq data. And I’ve just completed a RRBS analysis on bismark. So I got some text file results but I’m not quite sure how to interpret these data. What is the best tool to make them visual? Some of the…