raw-modifcation-calls-fixed-format.zip

Methylation calling of nanopore sWGS data. 5mC was called using DeepSignal Version: 0.1.8, with model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt, which was downloaded from the DeepSignal Google Drive (https://drive.google.com/open?id=1zkK8Q1gyfviWWnXUBMcIwEDw3SocJg7P). We used the DeepSignal call_mods (mofidication_call) output tsv file. To aid in combined methylation and fragmentomic analysis, we added additional columns to this file The final 14 fields were extracted from Minimap2 alignment files, matched by read id. They are as follows:Column 11: flag, 12: contig, 13: start, 14: end, 15: mapping quality of the chosen alignment, 16: mapping quality of the alignment with the best mapping quality (check), 17: mapping quality of the alignment with the "second" best mapping quality (check), 18: number of alignments for that read, 19: number of alignments for those alignments with mapping quality > 0, 20: left hard clipped bases, 21: left soft clipped bases, 22: read length (from CIGAR, not including soft clipped bases), 23: right soft clipped bases, 24: right hard clipped basesAll genomic coordinates are in GRCh38.