mRNA-Seq BY-COVID Pipeline: Counts
Version 1

Workflow Type: Galaxy
Work-in-progress

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

Inputs

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

Steps

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

Outputs

ID Name Description Type
html_report #main/html_report n/a
  • File
output_feature_lengths #main/output_feature_lengths n/a
  • File
output_short #main/output_short n/a
  • File

Version History

Version 1 (earliest) Created 19th Dec 2023 at 10:10 by Helena Rasche

Initial commit


Frozen Version-1 7f98d5d
help Creators and Submitter
Creators
  • Iacopo Cristoferi
  • Helena Rasche
Additional credit

Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter
Activity

Views: 1043

Created: 19th Dec 2023 at 10:09

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