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