An R markdown script for creating the output of NanoImprint. A tool for interpretation and visualization of DNA methylation at regions implicated in known imprinting disorders.
- For reference genome T2T-CHM13v2.0: Download NanoImprint_2_newbedfiles.Rmd and ctrls_2.xlsx
- For reference genome hg38: Download NanoImprint_Hg38_newbedfiles.Rmd and ctrls_hg38.xlsx. NOTE: Mapping to region H19/IGF2:IG-DMR is incomplete with hg38.
- Place the files in your data folder and open the NanoImprint script. Import your data BED files into the
#import datasection and run the script to produce an NanoImprint report. See output examples below.
Data requirements:
- Data should be obtained from modkit included in the Human variation workflow provided by ONTs epi2me labs. Both phased and unphased BEDMethyl files is required and should be created using the command line options
--modand--phasedin the Human variation workflow. - All three BED files must be sorted with BEDTools intersected before use. Sorting to the regions can be done using the region_T2T.bed or regions_hg38.bed:
bedtools intersect -a yourfile.methyl.cpg.acc.bed -b regions_T2T.bed > yourfile.methyl.filtered.bed
