Methylation Status of CpG islands for a specific gene
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2.9 years ago
kspata ▴ 70


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.

gene R BS methylKit Bismark • 642 views

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