db-GaP / GTEx analysis on the cloud. Easiest way?
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2.2 years ago

Hi!

I would like to analyze db-GaP data (in particular GTEx data); since i need to analyse WGS bams (600 samples), the total size would be overwhelming, so I wanted to do the analysis on the cloud.

Can anyone suggest me a platform that allows me to both use my own tools/pipeline and to get the files without downloading them?

I'm basically looking for something like Cancer Genomic Cloud (CGC, by sevenbridges).

I've already seen a couple of platform, from Google cloud/amazon AWS to DnaNexus but I don't have experience with them, and I cannot understand if it is possible to directly analyse the files, or you need to download them first.

Thank you very much in advance!

db-gap GTEx cloud amazon google • 1.1k views
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in particular GTEx data

Be ready to pay for access to that data if you are not going to use it on google cloud. Refer to this page for access instructions.

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2.2 years ago

The NCBI would like you to use the AnVIL service, which is hosted on the Google Cloud (US region).

The data itself is stored in a US region Google Cloud Bucket. Using it within US region GC is free, but data egress outside google or to another google region incurs a charge. About 8 cents a GB I seem to remember.

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Another cool thing about working with Google cloud and AnVil/Terra is that there maybe some already existing workflows workflows that conforms with GATK best practices alongside custom notebooks to facilitate your analysis!

https://anvil.terra.bio/#library/showcase

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I'm not so sure how "cool" it is. NCBI just added $15,000 to the cost of my research project.

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Thanks! Yep I knew about AnVIL, but (probably I'm doing it wrong) it seems to allow you only to use the "standard workflows" they provide, and not to use a custom one. There is a link to dockerstore for "additional workflow" but I cannot find a way to import one in my workspace. Also, I'm interested in WGS bams rather than RNA-seq, and unfortunately there seem to be only WGS data for grch38, while I need the hg19 version (which is still available through db-gap)

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