Platform for Drug Discovery


Bismark base multi sample comparison pipeline (PE, with RefFlat annotation)


Introduction


    This pipeline maps bisulfate NGS reads to a reference genome using Bismark and compare methylation rates among multiple samples.


    Input formatFASTQ, BED, genePred (refFlat)
    Library layoutPaired-end
    SpeciesUnspecified
    Execution timeAbout 5 hours (3 samples that contain about 4 million reads)

Inputs


    Raw NGS reads (FASTQ format, paired-end): 2-10

    Repeat region info (RepeatMasker BED file): 1

    • Check the dataset type explanation: bed

    CpG island region info (BED format): 1

    • Check the dataset type explanation: bed

    Annotation by RefFlat (RefFlat format): 1


Outputs


    Workflow

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    Report

    • Comparison result
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    Raw read level mapping status on Genome Explorer

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