Extracts methylation levels from Bismark-aligned bisulfite sequencing data to generate per-cytosine reports.
This skill provides specialized guidance for performing methylation calling on Bismark-aligned BAM files. It facilitates the extraction of per-cytosine methylation reports across various genomic contexts (CpG, CHG, and CHH) for both single-end and paired-end sequencing data. Users can generate bedGraph files for genome browser visualization, comprehensive coverage reports for downstream analysis in tools like methylKit, and conduct M-bias analysis to identify and mitigate systematic biases in methylation measurements.
Key Features
01Automated bedGraph and genome-wide cytosine report generation
02Comprehensive paired-end and single-end data processing
03Support for CpG, CHG, and CHH methylation context extraction
04M-bias analysis to detect and ignore systematic read-end biases
05Python integration for parsing Bismark coverage data using Pandas
062 GitHub stars
Use Cases
01Generating methylation tracks for visualization in IGV or UCSC Genome Browser
02Quality control of bisulfite sequencing libraries via M-bias profiling
03Preparing coverage summaries for differential methylation region (DMR) detection
