I'm looking at Reduced representation bisulfite sequencing (RRBS) data from ENCODE, and to align the FASTQ files I've used Bismark with Bowtie 1. When I load the resulting BAM file into
GenomicRanges, I get something like this:
> reads GRanges object with 2 ranges and 5 metadata columns: seqnames ranges strand | seq XM XR XG NM <Rle> <IRanges> <Rle> | <DNAStringSet> <character> <character> <character> <integer>  chrM [16523, 16558] - | ATAAAACCTA...CCCTTAAATA .....h........h.......z............. CT GA 3  chrM [16524, 16559] + | TAAAGTTTAA...TTTTAAATAA .....hh.......hhh.h.z...hhhh........ CT CT 11 ------- seqinfo: 25 sequences from an unspecified genome
For the read on the - strand (which is aligned to the "G->A"-converted reference), how should I compare methylation calls to those on the + strand, since they don't line up?
For example, the
z in the methylation string of the - strand is one position ahead of the
z in the + strand (which makes sense because of symmetric CpG methylation). But how should I determine whether these two methylation calls are "essentially the same" or not?