Tag: methylkit

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

“MethylKit” package for WGBS data 0 Hi I am working with WGBS data, There I am using MethylKit package for DMC analysis. Differential DNA methylation is usually calculated by comparing the proportion of methylated Cs in a test sample relative to a control. In simple comparisons between such pairs of…

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…

R encountered fatal error when using processBismarkAln in methylKit 2 Hi I am attempting to use methylkit to analyse my RRBS data but cannot seem to be able to import my files. I have .bam files generated from bismark. I read I can use function processBismarkAln to read these kind…

Interpreting the CpG pearson correlation plot 0 I have performed DMR analysis using Methylkit and have generated the correlation plot but i am not able to interpret it completely. Apart from the correlation % what do the bar plots, color and x and y axis signify? Differential-methylation • 33 views…

Implementing covariates in calculating differential methylation 0 Could someone please assist me with the implementation of covariates in the calculateDiffMeth function? I’ve been attempting to include parameters like age, BMI, and smoking status within a data frame while performing the calculation, but it keeps generating an error. The error message…

Query Regarding Outlier Removal in RRBS Data Analysis Using MethylKit 0 Is it necessary to remove outliers in RRBS data analysis using MethylKit, and if so, what is the recommended method for outlier removal? I’ve employed the clusterSamples and PCASamples functions to detect outliers in my methylbase object. However, I’m…

How to index genome file for MethylDackel? 0 I am running following script on my indexed and sorted bam file, but it is giving error on genome file. I indexed my genome file using both BWA index and samtools. (for both getting same error) MethylDackel extract -@ 20 –chunkSize 30000000…

Hi, I’m working with whole-genome EM-seq data from an experiment with two factors: Two genotypes (with contrasting response to a pathogen) Infected and non-infected Only one tissue and one time analyzed, with two biological replicates for each treatment combination. I would like to know: Which sites/regions are differentially methylated in…

DMR Analysis for RRBS: what annotation file to I use? 0 Hi, I’m interested in running a DMR analysis on RRBS data. I was wondering what type of annotation file I need for the program (i.e methylkit or others) to identify promoters vs introns etc. Would a gtf file be…

DNA Methylation output subtract 0 Hello all, I have whole genome bisulfite sequencing for two cell populations. One of my cell populations has “pure” cells (Pop1), while my second cell population has a mixture of two cells (Pop2) including cells from my first population. Is there a way to subtract…

Error: free(): invalid next size (fast) and Aborted (core dumped) while using R in Linux server 0 Hi, I am using R (v4.1) in my Linux server with Ubuntu 22.04.2. I want to use the function processBismarkAln from the package MethylKit to read my .sam files (output from BisMark). The…

The same qvalues are reported to different pvalues 2 Hi guys, I’m running MethylKit to find differently methylated CpG. I have three replicates in the control and three in the treatment. When I run the code myDiff=calculateDiffMeth(meth,mc.cores=4,method=”fdr”) and then hyper=getMethylDiff(myDiff,difference=10,qvalue=0.01,type=”hyper”) the output give me qvalues lower than pvalues. Some of…

Query regarding DNA Methylation Bisulfite Sequencing data analysis 0 Hi, I am working on DNA Methylation Bisulfite Sequencing data analysis using methylkit and genomation. I am facing an issue while annotating my differentially methylated gene data using annotatewithGeneparts function from genomation. Actually, the number of rows/entries in dist.to.tss sheet and…

Getting same value for start and end position, “DNA methylation” 1 While using methyl kit, I am getting similar start and end positions. Please help me to find a way to get different start and end positions. DNAmethylation methylkit • 32 views • link updated 17 minutes ago by ATpoint…

Chemicals Dimethyl sulfoxide (DMSO) was purchased from Sigma-Aldrich (St. Louis, MO, USA), and 5-aza-2′-deoxycytidine (5-aza-dc), trichostatin A (TSA), bisphenol A, benzo[a]pyrene (BaP), benzo[c]fluorene (BcF), and beryllium sulfate (BeSO4) were obtained from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). The SCREEN-WELL Cardiotoxicity Library was purchased from Enzo LifeScience Inc. (Supplementary Table…

I am facing a problem on getting the DGElist from the function of readbismark2dGE(). It didn’t show any error. output of bismark2DGE only shows Hashing, counting. I am using google colab to get more system RAM. I am using R version R4.2.3 and BiocManager 3.16. if (!requireNamespace(“BiocManager”, quietly = TRUE))…

How to find p-values for annotated methylated regions using methylkit and genomation 0 Hi everyone, Greetings! I am working on DNA methylation bisulphite sequencing data analysis using R (packages = methylkit and genomation). I’ve successfully found the top methylated regions and have annotated them. But now I want to know…

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

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…

DNA methylation batch effect remove 1 Hi, I’m studying about DNA methylation. I draw heatmap with beta-value, but there are batch effects.. How can I remove these cgID with studio R? DNA effect batch methylation • 24 views Can you explain what do you mean by ‘beta-value’? Generally batch effect…

Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file? 0 Hi. I am performing differential methylation analysis in grapevine (vitis vinifera). To annotate differentially methylated region or bases i need the annotation file i.e., bed file. From where should i find that annotation…

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….

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 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…

Using MethylKit with gemBS output files 0 Hi, I was just wondering if anyone is familiar with using gemBS output files for MethylKit such as the ones below *_3_lane_gembs_cpg.bed.gz *_3_lane_gembs_cpg.txt.gz With the following columns Contig Pos0 Pos1 Ref Call Flags Meth non_conv conv support_call total I tried running methylKit but…

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.,…

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…