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Benjamin P. Berman , Efrat Katsman , Filippo Martignano , Silvestro G. Conticello , Shari Orlanski ·

YOU? · · 2021 · Open Access · · DOI: https://doi.org/10.6084/m9.figshare.16823005 · OA: W4394393145

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.