Tag: Bismark
Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing
Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS Article Google Scholar Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…
Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark
Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark 0 Hello, previously, I was using Bismark with the ‘–comprehensive’ option to generate the individual bedgraph files from which we made the bigWigs. For one particular figure, my boss wants me to generate merged bdg files so that we…
From Bismark to methylkit, which file is better to use?
From Bismark to methylkit, which file is better to use? 1 Hi! I am trying to analyse some Bisulfite sequencing data files, but I am new to this sequencing analysis mode and I am a bit stuck. I have followed Bismark protocol for the alingment, deduplication and methylation extractor steps….
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),…
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…
Methylkit (differential methylation analysis) error in data frame
Methylkit (differential methylation analysis) error in data frame 0 Hi Friends, I am performing the differential methylation analysis using methylkit but it is throwing error in data frame. ” Error in [.data.frame(data, , 6) : undefined columns selected”. Can anyone help me to solve this error. Following is my R…
Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)
Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…
An epigenetic basis of inbreeding depression in maize
INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…
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…
