Google Cloud for RNA seq analysis
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10 weeks ago
John ▴ 220

Hi, Did anyone try Google Cloud Platform for RNA seq data analysis? They provide pipelines, how can I analyze without those pipelines.

Basically, I would like to do alignment using STAR, then peak calling using CLIPPer.

Thank you!

googlecloud gcp RNAseq Cloud • 251 views
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10 weeks ago

For RNA-seq analysis, you need access to Linux command-line programs such as aligners, assemblers, and R. So your best bet on google's cloud might be a virtual machine with access to the OS via command line. The product is called "compute engine". However, I was unsuccessful in activating the free-trial for that due to some errors on Google's side "The attempted action failed, please try again". Maybe it is just me or temporary today, but that put me off for now, it seems very buggy/alpha and definitely not re-assuring. You can try at https://cloud.google.com/compute and see if you can activate it.

Also, they require credit card information. If you want to continue using the cloud after your trial period, you better get a corporate credit card and calculate the costs for CPU and storage carefully.

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10 weeks ago
GenoMax 104k

Free tier is not going to cut it for actual samples/STAR alignments. You are looking at 30G of free RAM for STAR so the best option is to actually sign up for an account. That is pretty much is going to be true for all cloud providers. Ideally you would use an institutional account since it is easy to rack up costs if you are not careful.

That said, google compute gives you a bare VM with an OS of your choice. Ubuntu is one of the options and may be the easiest to deal with. Use conda/mamba to install programs and you would be on the way. If you are using human samples then keep local restrictions/policies about use of cloud resources in mind.

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