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Old 08-06-2018, 08:18 AM   #1
swan_r
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Location: North Carolina

Join Date: Apr 2012
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Question AWS for bioinformatics core

Hello,
Our department had started bioinformatics core recently and I am the only 1 bioinformatician there, we are looking for different options to run the analysis. We are planning to take AWS account, I have couple of questions of questions in my mind
1. Will there be any firewall problems when accessing the AWS from university.
2. If so, is it easier issue to resolve
3. How much space we need to run 200 RNA-Seq samples from AWS

Anyone has experience about this, I would really appreciate any feedback on this. Thank you.
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Old 08-10-2018, 05:58 PM   #2
brianytsui
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Location: UCSD, blog: https://brianyiktaktsui.wordpress.com

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1. Will there be any firewall problems when accessing the AWS from university.
There is no firewall by default on AWS. You can directly ssh from your computer to an EC2 instance. If you want better security, you can create something called a VPC with limited IP ranges.

3. How much space we need to run 200 RNA-Seq samples from AWS
If money is not an issue, EFS would be the most natural solution, as it grows and shrinks depending on the amount of data u put in, which means you don't have to think about the problem of scalability. I usually keep everything in the sorted bam format to keep the data small without losing anything. Most sorted RNAseq bams I have seen are less than 10GB in size, of course, it depends on a lot on the sequencing depth.

I just wrote a blog post about this kinda issue actually, hope it might be helpful :
https://brianyiktaktsui.wordpress.co...ing-the-cloud/
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