Platform for Drug Discovery



Bismark(SE)


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 paired-end read only
    SpeciesHuman(hg19)
    Execution timeAbout 6 hours. (3M paired-end reads[36bp+36bp]) x 2 samples

    Pipeline history
    Bismarkでマッピングを行いメチル化サイトを同定し、SAMtoolsのmpileupを用いてメチル化サイトの集計をします。
    さらにフィッシャーの正確確率検定(FET)による二群間比較を行い、レポートで結果を報告します。
    Image

Inputs

Outputs


    Image
    2サンプル間でCpGアイランド毎のメチル化率を比較解析した結果レポート


    Image
    Image
    Bismarkのメチル化検出結果(ゲノムビューワ表示)

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