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Old 02-11-2014, 04:20 PM   #1
inscent
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Location: California

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Default Running TopHat/Cufflinks on Google Compute Engine

Does anyone have any experience using the Google Compute Engine (or Amazon Web Services, or any other IAAS for that matter) to do RNA-Seq analysis with TopHat? The computers I have available are not at all suited to the task, and so I'd be interested to hear from anyone who has used one of these services.
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Old 03-28-2014, 08:18 AM   #2
scbody
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Default GoogleCompute

Hi
I'm also interested in hearing of anyone doing analyses on GoogleCompute. It seems much more functional and certainly cheaper now.
Thanks
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Old 03-28-2014, 01:26 PM   #3
mastal
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Default

I used Amazon Web Services EC2 to analyze some RNA-Seq data with Bowtie, Tophat and Cufflinks a few years ago.

I used a Ubuntu Linux ami, with 16 Gigabytes of ram, which doesn't seem like a lot now. I had files with 90 million 1X50 reads. I had started off with either a
4 Gb or 8 Gb machine, but got segmentation faults.

I just used a basic Linux ami, so I had to install all the bioinformatics software i wanted to use, like the Bowtie, Tophat, etc.
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Old 03-28-2014, 03:06 PM   #4
scbody
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Default Google Compute

Thanks for the information inscent.
Does anyone have information on recent use of the Google Compute?
Thank you
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