README.md

Workflows

This repository contains a collection of workflows created using the de.STAIR atoms. These are incorporated in the Galaxy workflow generator to provide a baseline of working use-cases, which users can adopt to familiarize with Galaxy tools for DGEA and RRBS/BS-Seq data analyses.

• Run workflows
• Contributed workflows
  • DGE analysis (single-end reads)
  • DGE analysis (paired-end reads)
  • RRBS/BS-Seq analysis (paired-end reads)

Run workflows

Workflows depend on their tools, which in turn are available depending on some Galaxy instances. For this reason, to make these workflows run it is important to make sure that you are running the Galaxy workflow generator, or any other instance that provides all necessary tools.

If you are using the Galaxy workflow generator, these tools are already included in the instance. From the header, click Workflow, and chose which one to run.
If you are not using the workflow generator, you have to download them, and upload them in your running instance.

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Contributed workflows

The Galaxy workflow generator provides workflows for DGEA and RRBS/BS-Seq data analyses.

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DGE analysis (single-end reads)

• FastQC, Cutadapt --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Cutadapt --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Cutadapt --> segemehl --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Cutadapt --> segemehl --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Cutadapt --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Cutadapt --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, PRINSEQ --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, PRINSEQ --> segemehl --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> segemehl --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, PRINSEQ --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> segemehl --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> segemehl --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> segemehl --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> segemehl --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2

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DGE analysis (paired-end reads)

• FastQC, Cutadapt --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2.ga
• FastQC, Cutadapt --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2.ga
• FastQC, Cutadapt --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2.ga
• FastQC, Cutadapt --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2.ga
• FastQC, Cutadapt --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2.ga
• FastQC, Cutadapt --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2.ga
• FastQC, PRINSEQ --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, PRINSEQ --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, PRINSEQ --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, PRINSEQ --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trimmomatic --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trimmomatic --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> BWA --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> BWA --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> HISAT2 --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> HISAT2 --> AWK, Infer Experiment, HTSeq-count, DESeq2
• FastQC, Trim Galore! --> STAR --> AWK, Infer Experiment, featureCounts, DESeq2
• FastQC, Trim Galore! --> STAR --> AWK, Infer Experiment, HTSeq-count, DESeq2

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RRBS/BS-Seq analysis (paired-end reads)

• FastQC, Cutadapt --> PRINSEQ --> Bismark --> SAMtools-filter, -sort, -fixmate, -markdup, -sort, MethylDackel, BEDtools-intersect intervals, -mergeBED, join, AWK
• FastQC, Cutadapt --> Trim Galore! --> Bismark --> SAMtools-filter, -sort, -fixmate, -markdup, -sort, MethylDackel, BEDtools-intersect intervals, -mergeBED, join, AWK
• FastQC, Cutadapt --> Trimmomatic --> Bismark --> SAMtools-filter, -sort, -fixmate, -markdup, -sort, MethylDackel, BEDtools-intersect intervals, -mergeBED, join, AWK

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