Tag: Bismark
which options to select with UMI-tools and BCLconvert for deduplication of reads
which options to select with UMI-tools and BCLconvert for deduplication of reads 0 Hi, I have paired-end RRBS data with a 6bp UMI encoded in the middle of the header made by our sequencing core using BCLconvert, looking like this (UMI in bold, index in italics): @A01685:159:H2YHFDSX7:4:2463:10655:16971:TAGCGC 1:N:0:CGTCTAAC After aligning…
bbduk command line options for EM-seq (NEB)
Hi I would like to use bbduk to replicate the command line flags used by trim_galore for EM-Seq (NEB). The bismark user guide recommends this for trim_galore –clip_R1 10 –clip_R2 10 –three_prime_clip_R1 10 –three_prime_clip_R2 10 Explanation of the trim_galore parameters –clip_R1 <int> Instructs Trim Galore to remove <int> bp from…
iGEM as a human iPS cell-based global epigenetic modulation detection assay provides throughput characterization of chemicals affecting DNA methylation
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…
Having problem on doing edgeR anlysis- cant create the DGE list through readbismark2DGE function.
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))…
Supported Tools – MultiQC
Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….
NGS: Sequence QC – Texas A&M HPRC
Back to Bioinformatics Main Menu Evaluation FastQC GCATemplates available: grace terra module spider FastQC After running FastQC via the command line, you can ssh to an HPRC cluster enabling X11 forwarding by using the -X option and view the images using the eog tool. From your desktop: ssh -X username@grace.hprc.tamu.edu From your FastQC working…
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome
Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…
Pig Reference Genome
Pig Reference Genome 1 What is the reliable source to download pig(Sscrofa) reference genome? I want to use it for bismark. Genome • 74 views • link updated 16 minutes ago by Ram 38k • written 2 hours ago by anasjamshed ▴ 120 Login before adding your answer. Traffic: 2668…
MethylR on bam files Gives Error
MethylR on bam files Gives Error 0 I used bismark to get bam files and now trying to implement processBismarkAln() on it but getting the following error: Using htslib. Error: Unexpected cigar: M As far as I know, some possible causes of this error could include: 1)A problem with the…
line 1 did not have 7 elements. –Putting bismark extractor files into methimpute
Error: line 1 did not have 7 elements. –Putting bismark extractor files into methimpute 0 file <- system.file(“extdata”,”file.txt”, package=”methimpute”) data(arabidopsis_chromosomes) arabidopsis_chromosomes$chromosome <- sub(‘chr’, ”, arabidopsis_chromosomes$chromosome) bismark.data <- importBismark(file, chrom.lengths=arabidopsis_chromosomes) I am trying to interpret my bismark results into methimpute but it gives me an error of : line 1 did…
–methimpute not recognized by Bismark and run in single core
Q: –methimpute not recognized by Bismark and run in single core 0 Q: –multicore not recognized by Bismark and run in single core /X/X/X/X/bismark/Bismark-0.24.0/bismark -s 0 -p 4 -u 0 -N 0 -L 20 –output_dir /X/X/X/X/X –nucleotide_coverage –genome_folder /X/X/X/X_ref -1 /X/X/X/X/X/X1.trim.fastq.gz -2 /X/X/X/X/X/X2.trim.fastq.gz Q: –methimpute not recognized by Bismark and…
Trying to calculate methylated C/All C , all output counts are 0
Trying to calculate methylated C/All C , all output counts are 0 0 Code: /X/X/X/X/bismark/Bismark-0.24.0/bismark_methylation_extractor –counts –comprehensive –multicore 8 X.bam /X/X/X/X/bismark2bedGraph CpG_file.gz -o file.bedGraph /X/X/X/X/coverage2cytosine–genome_folder ../X_ref file.bedGraph -o finalOut.txt bioinformatics RNA-seq error next-gen software sequence • 24 views Read more here: Source link
Bioconductor – DMRcaller
DOI: 10.18129/B9.bioc.DMRcaller This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see DMRcaller. Differentially Methylated Regions caller Bioconductor version: 3.12 Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is…
Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform
Background: Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising…
Transcriptional reprogramming of skeletal muscle stem cells by the niche environment
Isolation of pure populations of MuSCs and niche cells by fluorescence-activated cell sorting (FACS) Hindlimb muscles were dissected from young (4–6 weeks old) or aged (22–26 months old) C57BL/6J (Jackson Laboratory, 000664) mice and minced until no visible tissue chunks were visible. Muscle was then digested in a 15 ml Falcon…
Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform | BMC Bioinformatics
Comparison of read level and improving the mapping efficiency according to trimming Since the generation of high-quality WGBS data ultimately impacts the quantification and interpretation of Cs methylation levels, it is indispensable to monitor the raw data quality and interrogate the appropriate pre-processing step to cleanse data [1]. To avoid…
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves
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,…
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…
