Highlights

Here's a comprehensive overview of TwistNext DNA methylation sequencing analysis pipeline:

  1. READ_PROCESSING:

    • FASTQC: Performs quality control checks on raw sequence data.

    • TRIM_GALORE: Trims adapters and low-quality bases from the reads.

  2. BISMARK_ANALYSIS:

    • BISMARK_ALIGN: Aligns bisulfite-treated reads to a reference genome.

    • BISMARK_DEDUPLICATE: Removes PCR duplicates from the aligned reads.

    • SAMTOOLS_SORT: Sorts the aligned and deduplicated BAM files.

    • SAMTOOLS_INDEX: Indexes the sorted BAM files for efficient access.

    • QUALIMAP: Generates quality control metrics for the aligned reads.

    • BISMARK_METHYLATION_EXTRACTOR: Extracts methylation calls from the aligned reads.

    • BISMARK_REPORT: Generates a summary report of the Bismark alignment and methylation extraction.

  3. QC_REPORTING:

    • MULTIQC: Aggregates quality control reports from various steps into a single report.

  4. DIFFERENTIAL_METHYLATION:

    • EDGER_ANALYSIS: Performs differential methylation analysis using the EdgeR package.

    • METHYLKIT_ANALYSIS: Performs differential methylation analysis using the methylKit package.

  5. POST_PROCESSING: Generates summary statistics and visualizations of the differential methylation results.

  6. GO_ANALYSIS: Generates GOChord diagram from the gene ontology analysis results.

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