grouped-beta-value_bedgraph.zip

From the modified DeepSignal modification_call output described above (in “raw-modifcation-calls-fixed-format.zip”), we then extracted the methylation calls for each (strand-specific) CpG from column 9 (called_label field), and calculated a methylation beta value by taking the number of methylated reads (value 1) divided by the total number of reads (value 0 or value 1). These were collapsed into a bedgraph file with a value between 0-1 for every CpG covered. All genomic coordinates are in GRCh38.