Hi,

I am looking to obtain % Methylated C's for CpG islands for a specific gene. I have some BS converted PCR amplicon sequences sequenced on NextSeq PE150. I am using human genomic sequence for that particular gene X as a reference. I am using the following pipeline.

1. Raw Reads
2. bismark_genome_preparation
3. trim_galore
4. bismark (Output: bam file)
5. deduplicate_bismark ( Output: deduplicated bam)
6. bismark_methylation_extraction (Input: Deduplicated bam, Output: CpG report, bedGraph, Coverage, CpG_OT_report)

I want to further analyse the % of methylation for gene X. For that I have downloaded bed format for genomic regions for Gene X using UCSC genome browser.

Can you suggest me any approach to achieve this?

Thanks in advance.