RECLU ver3.0 (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 format | bam | ||
| Library layout | Single-end only | ||
| Species | human (hg19) only | ||
| Execution time | 6 hour (20M reads x 4 samples) | ||
Results
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Pipeline history
Table of contents
Inputs
- Multiple sorted alignment files in BAM format with the index files.
SAM/BAM Format Specification
- Multiple sorted alignment files in BAM format with the index files.
SAM/BAM Format Specification
Case samples: Case 1-10 (select two or more)
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Check the dataset type explanation: bam
Control samples: Control 1-10 (select two or more)
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Check the dataset type explanation: bam
Outputs
Clustering report
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Expression analysis report
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Motif discovery report
| Up regulated | Down regulated | ||
| Top peaks |
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| Bottom peaks |
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Options
Related information
Public
| samtools | Utilities for manipulating alignments in the SAM format. | (Original site) | (NGS Surfer's wiki) |
| BEDtools | A flexible suite of utilities for comparing genomic features. | (Original site) | (NGS Surfer's wiki) |
| R/edgeR | Empirical analysis of digital gene expression data in R | (Original site) | (NGS Surfer's wiki) |
| R/limma | Linear Models for Microarray Data | (Original site) | |
| AMD | De novo motif discovery tool | (Original site) | |
| WeederTFBS | Discover transcription factor binding sites (TFBSs) | (Original site) | |
| filo | Useful FILe and stream Operations | (Original site) | |
| MEME | Motif-based sequence analysis tools | (Original site) | (NGS Surfer's wiki) |
| DREME | Discriminative DNA motif discovery | (Original site) | |
| GLAM2 | Gapped local alignment of motifs | (Original site) | |
| paraclu | Finds clusters in data attached to sequences. | (Original site) | |
| FIMO | Find indivisual motif occurences | (Original site) |
RIKEN CLST Original
| symbolic_link_files.pl | |||
| automatedClustering0703 | |||
| plotNumberClusters.sh | |||
| plotStability.sh | |||
| automatedDE0703 | |||
| modifiedAutomatedPipelineMotifAnalysis0424 |