I have a region on the genome that was PCR amplified and bisulfite sequenced using ion-proton sequencer to detect methylation site. Can some one suggest how to align these reads back to the genome.
I came across BSSeeker however, their website do not work.... The deal here is it is just two regions on the genome that we are interested in, while most of the softwares are meant for the whole genome sequencing?
Any directions to detect methylation sites for such short stretches would be really great!