RNA Seq Reads To Counts
4.0

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Workflow Type: Galaxy

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1295?version=1

Inputs

ID Name Description Type
Input FASTQs collection Input FASTQs collection n/a
  • File[]
Input Reference gene BED Input Reference gene BED n/a
  • File

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


Open master 281f814
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
RSeQC
MultiQC
FastQC
Cutadapt
HISAT2
FeatureCounts
SAMtools
License
Creative Commons Attribution 4.0 International
Activity

Views: 320   Downloads: 93

Created: 25th Jun 2024 at 11:21

Last updated: 25th Jun 2024 at 11:21

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Total size: 156 KB
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