Hello all. I'd like to compare the speed for the tophat/cuffdiff protocol on various hardware platforms to see which is the speediest combination. Is there a small genome/sample set that anyone knows of that would be ideal for testing? The run should be quick (no more than 15 minutes per run) and ideally produce some differential expression data or at least be verified.
My default approach is going to be to use the genome I already have for my samples and then just chop off a small piece of left and right pair end reads (probably 10MB worth or so). I doubt I'll see anything interesting in the output but at least it will be a speed test.
Ideas are welcomed. Sorry if this question is naive, I'm just starting with RNA seq. Any information on speeding on rna seq would be welccomed. I just found STAR which looks interesting, but don't know much about it (http://gingeraslab.cshl.edu/STAR/).
My default approach is going to be to use the genome I already have for my samples and then just chop off a small piece of left and right pair end reads (probably 10MB worth or so). I doubt I'll see anything interesting in the output but at least it will be a speed test.
Ideas are welcomed. Sorry if this question is naive, I'm just starting with RNA seq. Any information on speeding on rna seq would be welccomed. I just found STAR which looks interesting, but don't know much about it (http://gingeraslab.cshl.edu/STAR/).
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