Description

1. READ_PROCESSING: Checks the quality of raw sequencing data and trims low-quality bases and adapters to improve downstream analysis.

2. BISMARK_ANALYSIS: Aligns bisulfite-converted reads to a reference genome, identifies and removes PCR duplicates, sorts and indexes the aligned reads, performs quality control on alignments, and extracts methylation information from the aligned reads.

3. QC_REPORTING: Compiles quality control metrics from various steps into a comprehensive report for easy interpretation.

4. DIFFERENTIAL_METHYLATION:

   • EDGER_ANALYSIS:

     • Takes coverage files, a design file, and comparison information as input.

     • Performs differential methylation analysis using the EdgeR Bioconductor package.

     • Outputs CSV files with differential methylation results for each group comparison. METHYLKIT_ANALYSIS:

     • Takes coverage files, a design file, and comparison information as input.

     • Performs differential methylation analysis using the EdgeR Bioconductor package.

     • Outputs CSV files with differential methylation results for each group comparison.

5. POST_PROCESSING:

   • Reads the EdgeR results and generates:

     • Summary statistics (total DMRs, hyper/hypomethylated regions, significant DMRs)

     • Volcano plot (visualizing fold change vs. significance)

     • MA plot (visualizing intensity vs. fold change)

6. Functional Analsysis

• Reads the EdgeR/MethylKit results and generates -

  • Top n corresponding genes from the EdgeR/MethylKit results are picked up to generate the gene ontology results.

  • generates a CSV file with the GO classification results (only Biological Processes).

  • generates a Chord diagram for top 10 results from the GO analysis.