Question: Do you recommend any platform that I can use instead of an HPC?
1
gravatar for ferro.d.bio
15 months ago by
ferro.d.bio10
ferro.d.bio10 wrote:

Hi all,

I need a little bit of help. I am currently working on the secondary analysis of RNAseq data, and I cannot use an HPC. Some of the data that I need to work on are from The database of Genotypes and Phenotypes (dbGaP). I am still waiting for my Pi to get access to the data of 600 patients, but in the meantime, I am working with SRAs. Do you recommend any platform that I can use instead of an HPC? I am thinking about cloud computing, but I have no idea what service to use and how much computational power purchases to have decent speed for using software such as Kallisto.

Thank you in advance, and have an awesome day!

Best, Diana

rna-seq snp variant analysis • 343 views
ADD COMMENTlink modified 15 months ago by Brice Sarver3.6k • written 15 months ago by ferro.d.bio10
1

Well, actually Kallisto can be ran on your laptop in notime, that's its entire purpose. Check out deploit https://deploit.lifebit.ai/app/home or firecloud by the Broad https://software.broadinstitute.org/firecloud/ they both supply an abstraction layer between your needs and the cloud. The process you should probably go through is defining a pipeline, either use an available one or build your own and then you can try and run this same pipeline in the cloud through these websites in an easy(er) way.

ADD REPLYlink written 15 months ago by Asaf8.5k
3
gravatar for Brice Sarver
15 months ago by
Brice Sarver3.6k
United States
Brice Sarver3.6k wrote:

Any of the cloud platforms will be able to do what you want, but you may have to have some hardware domain knowledge to configure the OS, install libraries, configure any permissions, etc.

You should look to spin up instances that are of the same size you'd expect to work on if you were connecting to bare-metal machines.

As one option, I'd recommend poking around on AWS' EC2 free tier and seeing whether you are comfortable enough with some basic system administration to configure an image and other instances. The m4.4xlarge instance size has been a workhorse for general, non-intensive bioinformatics work (16 vCPUs, 64 GiB RAM), though you can certainly go larger if you need more RAM. Less than a dollar an hour for a dedicated instance, not counting your storage.

ADD COMMENTlink modified 15 months ago • written 15 months ago by Brice Sarver3.6k
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