Hi, I have bisulfite converted sequencing reads and, from my bam file, would like to select reads that end at a Msp1 digest site (C^CGG). The way I would think to go about doing that is making a bed file of CCGG sites in the genome (from the fasta file) and then selecting reads from the bam file that end at those sites. However, I'm not sure how to do either part of this.
Can anyone help me out or do you have better ideas? Thanks!