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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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GoogleCompute
Hi
I'm also interested in hearing of anyone doing analyses on GoogleCompute. It seems much more functional and certainly cheaper now.
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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.Comment
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Google Compute
Thanks for the information inscent.
Does anyone have information on recent use of the Google Compute?
Thank youComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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