Hi,
I'm analysing some pair-end RNA-seq data from 20 healthy individuals using Tophat and Cufflinks. However, the novel isoforms detected from each individual are quite different from each other when I compared them across individuals. So now I'm thinking merging these 20 samples together into one mega file, and then use Tophat and Cufflinks to detect isoforms. This brings with a new problem. The mega file is very big, about 74G for read1 and another 74G for read2. When I ran Tophat, it took me about three weeks, and this is very risky because if for any reason my computer was shut down, my job was terminated and I need to tun it again. Does anyone know how to make tophat run quicker for this kind of large input files?
Many thanks
I'm analysing some pair-end RNA-seq data from 20 healthy individuals using Tophat and Cufflinks. However, the novel isoforms detected from each individual are quite different from each other when I compared them across individuals. So now I'm thinking merging these 20 samples together into one mega file, and then use Tophat and Cufflinks to detect isoforms. This brings with a new problem. The mega file is very big, about 74G for read1 and another 74G for read2. When I ran Tophat, it took me about three weeks, and this is very risky because if for any reason my computer was shut down, my job was terminated and I need to tun it again. Does anyone know how to make tophat run quicker for this kind of large input files?
Many thanks
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