mRNA-Seq BY-COVID Pipeline: Counts
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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/1001?version=1

Inputs

ID Name Description Type
UCSC Genome UCSC Genome Export of UCSC Genome, just the genes.
  • File
mRNA-Seq Reads mRNA-Seq Reads Input list of fastqsanger format sequencing data
  • File[]

Steps

ID Name Description
2 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
3 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0
4 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
5 FastQC (Post-cleaning) toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
6 HISAT2 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1
7 Relabel identifiers __RELABEL_FROM_FILE__
8 featureCounts toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1
9 Read Distribution toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2
10 Gene Body Coverage (BAM) toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2
11 FastQC (Pre-cleaning) toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
12 Multi QC raw reads toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1

Outputs

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

Version History

0 (earliest) Created 22nd Apr 2024 at 11:17 by Helena Rasche

Added/updated 3 files


Open master f673307
help Creators and Submitter
Creators
  • Iacopo Cristoferi
  • Helena Rasche
Additional credit

Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter
Tools
Cutadapt
FastQC
HISAT2
FeatureCounts
RSeQC
MultiQC
License
GNU General Public License v3.0 or later
Activity

Views: 458   Downloads: 106

Created: 22nd Apr 2024 at 11:17

Last updated: 22nd Apr 2024 at 11:17

help Attributions

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Total size: 25.7 KB
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