master	develop

GUDMAP/RBK RNA-Seq Pipeline

Introduction

This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.

To Run:

• Available parameters:
  • --deriva active credential.json file from deriva-auth
  • --bdbag active cookies.txt file from deriva-auth
  • --repRID mRNA-seq replicate RID
    note: once deriva-auth is run and authenticated, the two files above are saved in ~/.deriva/ (see official documents from deriva on the lifetime of the credentials)
• FULL EXAMPLE:

  nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA

CHANGELOG

Credits

This worklow is was developed by Bioinformatic Core Facility (BICF), Department of Bioinformatics

PI

Venkat S. Malladi
Faculty Associate & Director
Bioinformatics Core Facility
UT Southwestern Medical Center
orcid.org/0000-0002-0144-0564
venkat.malladi@utsouthwestern.edu

Developers

Gervaise H. Henry
Computational Biologist
Department of Urology
UT Southwestern Medical Center
orcid.org/0000-0001-7772-9578
gervaise.henry@utsouthwestern.edu

Jonathan Gesell
Computational Biologist
Bioinformatics Core Facility
UT Southwestern Medical Center
orcid.org/0000-0001-5902-3299
johnathan.gesell@utsouthwestern.edu

Jeremy A. Mathews
Computational Intern
Bioinformatics Core Facility
UT Southwestern Medical Center
orcid.org/0000-0002-2931-1430
jeremy.mathews@utsouthwestern.edu

Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).