Platform for Drug Discovery


RECLU ver3.1 (RIKEN CLST)


Introduction


    The RECLU(REproducible CLUStering method) pipeline implements clustering, differential expression analysis, and motif discovery analysis. The pipeline uses the Paraclu program and the IDR script for clustering, the differentially expressed genes with < 0.05 p-value and > 2.0 absolute log fold-change are detected by the edgeR package. The AMD, GLAM2, Weeder and DREME programs are used for searching motifs&##044; and the Fimo program scans for occurrences of the motifs in the pipeline. The pipeline allows BAM files as input files.


    Input formatbam
    Library layoutSingle-end only
    SpeciesHuman(hg19), Mouse(mm9), Rat(rn4), Chicken(galGal3), Dog(canFam2)
    Execution time22 hour (20M reads x 8 samples)


    Results
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    Pipeline history
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Inputs


    Case samples: Case 1-10 (select two or more)

  • Check the dataset type explanation: bam
    Multiple sorted alignment files in BAM format with the index files.
    SAM/BAM Format Specification

  • Control samples: Control 1-10 (select two or more)

  • Check the dataset type explanation: bam
    Multiple sorted alignment files in BAM format with the index files.
    SAM/BAM Format Specification

Outputs


    Clustering report

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    Expression analysis report

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    Motif discovery report

    Up regulatedDown regulated
    Top peaks Image Image
    Bottom peaks Image Image

Options

Related information

References