Platform for Drug Discovery



TopHat2-Cuffdiff for known gene/isoform expression comparison pipeline (less than 10 N=1 paired-end fastq files)


Introduction


    Detect DEG (differentially expressed genes) at a known gene level and a known isoform level. Map short reads to reference genome by using TopHat2. Detect DEG by cuffdiff.<br/>


    Input formatFASTQ (Illumina)
    Library layoutFor paired-end read only
    SpeciesHuman(hg19),Mouse(mm9),etc.
    Execution timeAbout 14hours. (3 samples)

    Results
    Image

    Pipeline history
    Image

Inputs


    Input1-10: paired-end sequence fastq file.
    Input11: GTF annotation file for known gene/isoform.
    Input12: Always you do not have to set this. This is used for null input.

Outputs


Options


Comments


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