RNAseq_UMG_SDumont_v1
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.

Inputs

ID Name Description Type
GTF File GTF File n/a
  • File
KO Fastq Files KO Fastq Files n/a
  • File[]
WT Fastq Files WT Fastq Files n/a
  • File[]

Steps

ID Name Description
3 Align WT toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
4 Align KO toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
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/deseq2/2.11.40.6
8 CreateFilterOnCountsNA Filter1
9 CreateFilterOnCountsC7 Filter1
10 CreateSortOnCounts sort1

Outputs

ID Name Description Type
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File

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
Creator
Submitter
Citation
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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