About swDMR - xflicsu/swDMR GitHub Wiki

Welcome to the swDMR wiki!

About swDMR

swDMR is a sliding window approach, which is used to identify differentially methylated regions (DMR) from bisulfite sequencing dataset at single base resolution. The dataset, like whole genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) with the same coverage region of samples, are suitable for swDMR. This software integrated several useful statistics methods, satisfying to two or multiple samples test. In addition, swDMR provides genomic features annotation with BED or GFF file. It can also produce WIG format file to upload to UCSC genome browser for DMR visualization.

Input of swDMR

Input methylation file format: must contain follow information (separated by table "\t")

you can assign the corresponding information contained in your files

information required: chromosome position ctype methyl_reads unmethy_reads

Output of swDMR

"swDMR.for.low.Extend" is the final result file containing DMR information of your comparison.

detail information: #chromosome, DMR_start, DMR_end, CpGs_number(or CHH/CHG), methylation_level_A, methylation_level_B, mean_depth_A, mean_depth_B, p_value