cleantranscriptfile
cleantranscriptfile cleans and formats transcript files to produce S-MART-compatible inputs for analysis of RNA transcripts generated by next-generation DNA sequencing.
Key Features:
- Data refinement: Cleans and formats transcript records to conform to S-MART input requirements.
- S-MART compatibility: Produces output formatted for direct use with S-MART (Sequence-based Meta-Analysis of RNA Transcripts).
- Reproducible processing: Applies a consistent automated cleaning procedure that minimizes manual intervention and supports reproducible tracking of file modifications.
Scientific Applications:
- Biomedical research: Prepares transcript data from next-generation sequencing for analyses relevant to gene expression and transcriptomics studies.
- Large-scale RNA meta-analyses: Enables aggregation and meta-analysis of RNA transcripts using S-MART to study gene expression patterns and regulatory mechanisms.
Methodology:
Automates the cleaning and formatting of transcript files to meet S-MART input specifications, minimizing manual intervention and reducing formatting-related errors.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 11/25/2024
Operations
Data Inputs & Outputs
Sequence file editing
Inputs
Publications
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.