Version 1

Workflow Type: Galaxy

RNAseq workflow UMG: Here we introduce a scientific workflow implementing several open-source software executed by Galaxy parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a configurable script code.


ID Name Description Type
GTF File GTF File n/a
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KO Fastq Files KO Fastq Files n/a
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WT Fastq Files WT Fastq Files n/a
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ID Name Description
3 Align WT toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/
4 Align KO toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/
5 Counts WT toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1
6 Counts KO toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1
7 DE Analysis WTvsKO toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/
8 CreateFilterOnCountsNA Filter1
9 CreateFilterOnCountsC7 Filter1
10 CreateSortOnCounts sort1


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_anonymous_output_16 _anonymous_output_16 n/a
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_anonymous_output_17 _anonymous_output_17 n/a
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Version History

Version 1 (earliest) Created 6th Dec 2022 at 19:22 by Kary Ocaña

Initial commit

Frozen Version-1 fc807ec
help Creators and Submitter
Ocaña, K. (2022). RNAseq_UMG_SDumont_v1. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.412.1

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Created: 6th Dec 2022 at 19:22

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