04-07-Pipeline-ways-to-run-a-pipeline.Rmd

# Where / how can I run an RNA-seq pipeline ? {-}

At Monash:

Web-based:

- Laxy.io / Degust
- Galaxy Australia

Command line:

- M3 / Monarch HPC clusters
- NeCTAR virtual machine (~32 - 64Gb RAM)
- Your laptop .. _while not recommended, you may be able to do this for smaller genomes (bacteria, yeast), and larger genomes if using the Salmon pseudo-mapping protocol_