Category: methylkit

DNA methylation batch effect remove

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…

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Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file?

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…

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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….

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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…

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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…

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Using MethylKit with gemBS output files

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…

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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.,…

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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…

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