RNA Seq Reads To Counts 4.0
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Run on GalaxyRNA-Seq reads to counts
Associated Tutorial
This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, Harriet Dashnow
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input FASTQs collection | Input FASTQs collection | n/a |
|
| Input Reference gene BED | Input Reference gene BED | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Infer Experiment | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 |
| 11 | Read Distribution | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1 |
| 12 | Column Join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 13 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 |
| 2 | FastQC raw reads | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 |
| 3 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 |
| 4 | FastQC post QC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 |
| 5 | HISAT2 | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 |
| 6 | featureCounts | toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3 |
| 7 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 |
| 8 | Samtools idxstats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2 |
| 9 | Gene Body Coverage (BAM) | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3 |
Version History
master
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Views: 54 Downloads: 7 Runs: 0
Created: 2nd Jun 2025 at 11:04
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