Tag: RRBS

re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k,…

Continue Reading re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

Postdoc position in circadian biology and bioinformatics

We are seeking a highly motivated and dynamic researcher with expertise in analysis and interpretation of high-throughput sequencing (transcriptomics, epigenomics etc.) and mass spectrometry (proteomics, metabolomics etc.) to work in the Zierath Group in collaboration with Barrès Group and Deshmukh Group. The position is a 3-year position to start March…

Continue Reading Postdoc position in circadian biology and bioinformatics

Introduction to DNA Methylation Analysis: From Wet Lab Experiments to Bioinformatics Analysis

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…

Continue Reading Introduction to DNA Methylation Analysis: From Wet Lab Experiments to Bioinformatics Analysis

DNA Methylation Sequencing market to showcase strong CAGR between 2028 and 2028

The business intelligence report on the DNA Methylation Sequencing market provides investors a tactical advantage by focusing on the growth trajectory of this business vertical during 2022–2028 through a thorough assessment of the historical and current trends. The estimations in the document have also been calculated and verified by professionals…

Continue Reading DNA Methylation Sequencing market to showcase strong CAGR between 2028 and 2028

A mammalian methylation array for profiling methylation levels at conserved sequences

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…

Continue Reading A mammalian methylation array for profiling methylation levels at conserved sequences

ChaoXianSen/TrimGalore – Giters

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…

Continue Reading ChaoXianSen/TrimGalore – Giters

“Normal” percent duplication for RRBS reads?

“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…

Continue Reading “Normal” percent duplication for RRBS reads?

RnBeads Stuck in “STARTED Methylation Value Distributions

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…

Continue Reading RnBeads Stuck in “STARTED Methylation Value Distributions

MethylDackel Error running on HPC server

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…

Continue Reading MethylDackel Error running on HPC server

RRBS methylation analysis

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…

Continue Reading RRBS methylation analysis

Medical College of Wisconsin hiring Bioinformatics Analyst I in Milwaukee, Wisconsin, United States

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….

Continue Reading Medical College of Wisconsin hiring Bioinformatics Analyst I in Milwaukee, Wisconsin, United States

Advice on RRBS analysis software : bioinformatics

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…

Continue Reading Advice on RRBS analysis software : bioinformatics

Bioinformatics Scientist in Diagenode – GrabJobs

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…

Continue Reading Bioinformatics Scientist in Diagenode – GrabJobs

Difference in Bismark output methylation call files and coverage files

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),…

Continue Reading Difference in Bismark output methylation call files and coverage files

Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

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…

Continue Reading Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

Bioinformatics Analyst II – Job at Medical College of Wisconsin in Menomonee Falls, WI

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…

Continue Reading Bioinformatics Analyst II – Job at Medical College of Wisconsin in Menomonee Falls, WI

RRBS data analysis using Bismark and methylkit

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…

Continue Reading RRBS data analysis using Bismark and methylkit

Bismark rrbs data analysis

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…

Continue Reading Bismark rrbs data analysis