Workflow Type: Galaxy
Open
RNA-Seq reads to counts
Associated Tutorial
This workflows is part of the tutorial 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
4.0 (earliest) Created 25th Jun 2024 at 11:21 by Helena Rasche
Added/updated 4 files
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Views: 133 Downloads: 45
Created: 25th Jun 2024 at 11:21
Last updated: 25th Jun 2024 at 11:21
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