Platform for Drug Discovery



Bismark(PE)


Introduction


    This pipeline detect methylation site in CpG, ChG and CHH context. And get the region that is obviously different methylation rate among two samples.


    Input formatFASTQ(Illumina, IonTorrent, etc...)
    Library layoutFor single-end read only
    SpeciesHuman(hg19)
    Execution timeAbout 6 hours. (3M paired-end reads[36bp+36bp]) x 2 samples

    Pipeline history

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Inputs

Outputs


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    Bismark methylation result

Options


Comments


Use case


Related information


    Public
    #Tool nameLink to original siteLink to our wiki site
    1Bismark(Original site) (NGS surfer's wiki)
    2SAMtools(Original site) (NGS surfer's wiki)
    3BEDtools(Original site) (NGS surfer's wiki)


    Private
    #Script nameDescription
    1bismarkSamToMetSamLike.plForced to assign methylation information with ATGC to pile up by SAMtools
    2callMethtlBaseFromMpiliup.plConvert pileupped ATGC to methylation count file
    3bismarkSamToGeTsv.plConvert bismark output file to data for our genome browser: Genome Explorer
    4convertMethylBasesInfToGeTsv.plConvert pileupped information to methylation rate track and methyl-C/non-metyl-C count track for Genome Explorer
    5load_gbmap_data.plLoad data for Genome Explorer
    6mergeBasalVarInfToRegionalVarInf.shMerge two mathylation count files
    7sumUpVarInfOutFromIntersec.plSum up merged methylation count file per genomic features as like CpG island region information
    8varRateTestWithFET.shTest two samples of methyl-C/non-methyl-C counts by FET:Fisher's Exact Test
    9FETtestedRegionalVarInfToHtml.plMake HTML report to display the test result