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RNAseq

README.md

GeneLab bioinformatics processing pipelines for Illumina RNA-sequencing data

Documents GL-DPPD-7101-G.md and GL-DPPD-7115 contain overview and example commands for how GeneLab processes RNAseq datasets from eukaryotic and prokaryotic organisms, respectively. See the Repository Links descriptions below for more information. Processed data output files and a GeneLab data processing summary is provided for each GLDS dataset in the Open Science Data Repository (OSDR).

RNAseq Processing Pipelines

Eukaryotes

Eukaryotic RNAseq processing workflow

Prokaryotes

Prokaryotic RNAseq processing workflow

Repository Links

  • Pipeline_GL-DPPD-7101_Versions

    • Contains the current and previous GeneLab RNAseq consensus processing pipeline (RCP) versions documentation for eukaryotic organisms

  • Pipeline_GL-DPPD-7115_Versions

    • Contains the current and previous GeneLab RNAseq consensus processing pipeline (RCP) versions documentation for prokaryotic organisms

  • RNAseq_Tool_Install

    • Contains instructions and associated yaml files to install the conda environments containing tools used to process RNAseq datasets using the GeneLab RCP, versions A-E

  • GeneLab_Reference_and_Annotation_Files

    • Contains links to the fasta and gtf annotation files used to process RNAseq datasets using the GeneLab RCP, versions A-E

      Note: Reference annotation files used from RCP version F and onward are documented in GeneLab_Reference_Annotations

  • Workflow_Documentation

    • Contains instructions for installing and running the GeneLab RCP workflow

      Note: The RCP workflow was implemented beginning with RCP version F

  • GLDS_Processing_Scripts


Licenses

The software for the RNAseq pipeline and workflow is released under the NASA Open Source Agreement (NOSA) Version 1.3.

3rd Party Software Licenses

Licenses for the 3rd party open source software utilized in the RNAseq pipeline and workflow can be found in the 3rd_Party_Licenses sub-directory on the GeneLab_Data_Processing GitHub repository landing page.


Notices

Copyright © 2025 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. All Rights Reserved.

Disclaimers

No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE. FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE, AND DISTRIBUTES IT "AS IS."

Waiver and Indemnity: RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT. IF RECIPIENT'S USE OF THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT, TO THE EXTENT PERMITTED BY LAW. RECIPIENT'S SOLE REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL TERMINATION OF THIS AGREEMENT.

The "GeneLab RNA Sequencing Processing Pipeline and Workflow" software also makes use of the following 3rd party Open Source software, released under the licenses indicated above. A complete listing of 3rd Party software notices and licenses made use of in "GeneLab RNA Sequencing Processing Pipeline and Workflow" can be found in the RNAseq_3rd_Party_Software.md file as indicated above.


Developed by:
Amanda Saravia-Butler
Jonathan Oribello

Maintained by:
Alexis Torres
Crystal Han