Platform for Drug Discovery



nAnT-iCAGE (RIKEN CLST) v1.4 TopHat


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
    Library layoutSingle-end
    SpeciesHuman, Mouse, Rat, Chicken, Dog, Caenorhabditis elegans
    Execution timeAbout 22 hours (30M single-end reads[54bp])

Inputs


    Raw NGS reads (FASTQ format, Single-end): 1

    惻Check the dataset type explanation: fastq (single-end)

Outputs


    Image
    CTSS results (BED format)
    Image
    Genome Explorer

    Image
    Mapping report
    Image
    Mapping report (remove PCR duplication)

    Image
    raw base distribution
    Image
    base N distribution
    Image
    rRNA base distribution


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


    Image
    mapping summary

Related information