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Table 1 Sample text file that can be read by methylKit.

From: methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

chrBase chr base strand coverage freqC freqT
chr21.9764539 chr21 9764539 R 12 25 75
chr21.9764513 chr21 9764513 R 12 0 100
chr21.9820622 chr21 9820622 F 13 0 100
chr21.9837545 chr21 9837545 F 11 0 100
chr21.9849022 chr21 9849022 F 124 72.58 27.42
chr21.9853326 chr21 9853326 F 17 70.59 29.41
  1. methylKit can read tab-delimited text files with the following format: the text fileshould include a unique.id, chromosome name, base position, strand, read coverage, % of C bases and% of T bases on that location.