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Old 04-06-2011, 01:25 PM   #1
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Location: US

Join Date: Apr 2011
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Default cap3 and pcap question

I am using cap3 for assembling my 454 RNA-seq reads. It turns out the unparallelized cap3 is too slow (already taking 10 days) given the size of my data (300MB), and I am thinking of using pcap instead of cap3 for my assembly.

However, I am not sure whether it's justifiable to use pcap instead of cap3 for EST assembly, since pcap is a genome assembler. Is there any assumption in pcap violating the principle of EST assembly?

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