Project title
Standardised processing of cancer cohort RNA-seq data for streamlined analysis and discovery
Collaborators and funding
Contact(s)
Andrew Lonsdale, Peter MacCallum Cancer Centre, andrew.lonsdale@petermac.org
Project description and aims
Leveraging these summarised databases effectively with patient and research cohorts requires private RNA-seq samples to be processed using the same pipelines. The Snapcount and Recount3 common backend workflow differs from clinical and standard pipelines, and requires raw data to be reanalyzed and processed to directly comparable with the pre-computed public databases. The goal of this project is to develop a systematic method to: transfer files to national compute, process private samples using a common workflow, summarise at cohort level, and export results back for analysis.
How is ABLeS supporting this work?
This project is supported by the Production Bioinformatics scheme provided by ABLeS, providing access to compute and storage resources at the Pawsey Supercomputing Research Centre.
Expected outputs enabled by participation in ABLeS
The major outcome of this project would be a Snapcount3 compatible resource via a Snaptron server. This will give an API for querying splicing and metadata across across. paediatric caner cohorts for researchers to use. This will result in both a web accessible database for querying, and an associated paper disseminating key findings. A Snaptron web service running under Docker will be deployed on institutional virtual machines to store and disseminate the data.
These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.