Goal: is to analyze bisulife sequencing data from .bam files
The first data received are deep-sequencing of 38 amplicon regions. We want to call DNA methylation haplotypes from these files.
Step 1. Summarize these 38 amplicon regions.
Step 2. Clip the regions from the C of the first CpG to the G of the last CpG.
Step 3. Read a .bam file, require the read to cover the entire clipped region, call the (complete) haplotypes, and write to Excel file.
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