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Old 02-25-2013, 02:23 PM   #1
jsimba
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Location: Australia

Join Date: Feb 2013
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Default Improve capacity for tophat analysis

Hi every one,

I am running Tophat for my RNAseq analysis but Im facing troubles of capacity of my platform OsX, It started 3 days ago and then suddenly the computer turned off so I began the command again. My question is whether is there any way to improve the performance? or does it depends od the size of the files?

thanks
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Old 02-25-2013, 05:48 PM   #2
vinay052003
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Location: Atlanta, US

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Default

Computing time of TopHat can be improved by first aligning your reads to the transcriptome rather than the whole genome. Then align rest of the reads to the genome. TopHat has inbuilt capability for doing that automatically. check -G option in the tophat manual.

If you are worried about RAM, then you can either split up your fastq files, run tophat separately and then merge and coordinate sort the bam files in the end.
Or you could run tophat for each chromosome separately. Current version of TopHat is pretty efficient in the memory usage anyways. So I wouldn't worry much about that.
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