Platform for Drug Discovery



RECLU ver3.4 (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, 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
    Specieshuman
    Execution time6 hour (20M reads x 4 samples)

Table of contents

Inputs


    Case sample mapping data (BAM format): 2-10

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

    Control sample mapping data (BAM format): 2-10

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

Outputs


    Clustering report

    Image Image


    Expression analysis report

    Image Image


    Motif discovery report

    Up regulatedDown regulated
    Top peaks Image Image
    Bottom peaks Image Image

Options


Comments


    ・Input BAM files require to be sorted.
    ・BAM files that are produced through nAnT-iCAGE (RIKEN CLST) TopHat pipeline are recommended as input files.

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