Platform for Drug Discovery



nAnT-iCAGE v1.1


Introduction


    A mapping pipeline for nAnT-iCAGE protocol. bwa is used for mapping. When barcode information is empty, extraction step will be skipped. This pipeline can't handle library with mixed genome.


    Input formatFASTQ(Illumina, etc...)
    Library layoutFor single-end read only
    SpeciesHuman(hg19), Mouse(mm9), Mouse(mm10), Rat(rn4), Chicken(galGal3), Dog(canFam2), Caenorhabditis elegans(ce10)
    Execution timeAbout 22 hours (30M single-end reads[54bp])

    Results
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    CTSS results(BED format)
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    Genome Explorer
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    Mapping report

    Workflow
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Inputs

Outputs


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    CTSS results(BED format)
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    Genome Explorer

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    Mapping report
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    Mapping report(remove PCR duplication)

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    raw base distribution
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    base N distribution
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    rRNA base distribution


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    no barcode sequence top100
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    rRNA sequence top100
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    mapped sequence top100
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    unmapped sequence top100


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    mapping summary


Options


Use_case


Related information