Tag: WGBS

Interpreting TFBS enrichment from random genomic regions

Hi all, To make a long story short, my lab has developed a computational method for analyzing WGBS data that results in genomic regions of interest. These are regions defined by sequencing reads with mixed methylation states (i.e. consecutive CpGs having non-matching methylation). My boss wants me to use some…

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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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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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Downloading WGBS sequencing reads for cancer sample and healthy sample

Downloading WGBS sequencing reads for cancer sample and healthy sample 0 Hello, I am completely new in WGBS data analysis. I want to learn analysing differentially methylated regions between cancer and normal sample. How can I find these data easily? I’m looking for WGBS reads data. Your help is highly…

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Allele-Specific analysis for human WGBS data

Allele-Specific analysis for human WGBS data 0 Hi everyone, I need to perform allele-specific methylation analysis for human whole genome bisulfite sequencing data. As Allele-specific analysis is dependent on SNPs/Polymorphic sites, I stuck with two queries: Is there a way to get these polymorphic sites from WGBS data ? (I…

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