wgbstools bam2pat Sigmoid_Colon_STL003.bam # output: # Sigmoid_Colon_STL003.pat.gz # Sigmoid_Colon_STL003.beta Once you have pat and beta files, you can use wgbstools to visualize them. For example: wgbstools vis Sigmoid_Colon_STL003.pat.gz -r chr3:119528843-119529245 wgbstools vis ...
For example, if site CpG100 appeared 510 times, from which 100 times it was methylated, the 100'th row will be (50, 255). We find it negligible for most cases, but if you find it important, use the lbeta format (wgbstools pat2beta --lbeta ARGS...)...
wgbstools bam2pat Sigmoid_Colon_STL003.bam#output:#Sigmoid_Colon_STL003.pat.gz#Sigmoid_Colon_STL003.beta Once you havepatandbetafiles, you can use wgbstools to visualize them. For example: wgbstools vis Sigmoid_Colon_STL003.pat.gz -r chr3:119528843-119529245 ...