mRNA-Seq BY-COVID Pipeline: Counts
1.0

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Workflow Type: Galaxy

This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.

Associated Tutorial

This workflows is part of the tutorial mRNA-Seq BY-COVID Pipeline: Counts, available in the GTN

Tutorial Author(s): Marek Ostaszewski, Matti Hoch, Iacopo Cristoferi, Myrthe van Baardwijk, Saskia Hiltemann, Helena Rasche

Tutorial Contributor(s): Helena Rasche, Matti Hoch, Mira Kuntz, José Manuel Domínguez, Sanjay Kumar Srikakulam, Björn Grüning

Workflow Author(s): Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Funder(s): BeYond-COVID

SEEK ID: https://dev.workflowhub.eu/workflows/1327?version=1

ID	Name	Description	Type
UCSC Genome	#main/UCSC Genome	Export of UCSC Genome, just the genes.	File
mRNA-Seq Reads	#main/mRNA-Seq Reads	Input list of fastqsanger format sequencing data	array containing File

ID	Name	Description
2	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
3	Cutadapt	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0
4	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
5	HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1
6	featureCounts	toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1
7	Read Distribution	toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2
8	Gene Body Coverage (BAM)	toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2
9	Multi QC raw reads	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1