Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Video: Visualization of whole genome DNA methylation data in IGB
Using PhiX to estimate bisulfite conversion rate
Which statistics should be applied to determine whether a region is differentially methylated or not?
Why would there be a large bias in number in the negative and positive strand after aligning with Bismark?
WGBS alignment with BitMapperBS
Bismark bug in BS-seq alignment
BAM Flag From Bismark Alignment: Forward and Reverse Chain
Methylation frequency + and - strand
Possible bug for bismark when methylation calling ?
Any reason for higher reported levels of non-CG methylation when analysing non-directional WGBS libraries with Bismark?
Newbie questions about Methyl-Seq (Bismark)
BS-seq: Using single end vs paired end in Bismark when Mapping efficiency is low
Bismark on sample with 2 genomes
Question: Best Practices/Softwares to filter methylation result of bismark?
Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Methylation Extractor report missing Chr annotation
Bismark returning alignments with no chromosome, Picard not happy.
Conversion effinciency issue in whole genome bisulfite sequencing data.
Question about galaxy tool wrapper
Bismark reads failing to align