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jflowers002 · 10-31-2013, 10:55 AM

Well, I will answer my own question. One inherent issue that i believe caused this trouble was my blast parameters. I had 100 genomes and I only allowed 250 hits since I was concerned about diskspace and time. Orhtomcl acutally recommends not limiting this (https://docs.google.com/document/d/1...xqDAMjyP_w/pub).

I figured that 2.5 orthologs in each genome for the same gene was enough, but maybe not. I am currently rerunning the process with a larger allowed hits and hopefully this will fix it.

10-31-2013, 10:55 AM	#2
jflowers002 Junior Member Location: Seattle Join Date: Jan 2013 Posts: 6	Well, I will answer my own question. One inherent issue that i believe caused this trouble was my blast parameters. I had 100 genomes and I only allowed 250 hits since I was concerned about diskspace and time. Orhtomcl acutally recommends not limiting this (https://docs.google.com/document/d/1...xqDAMjyP_w/pub). I figured that 2.5 orthologs in each genome for the same gene was enough, but maybe not. I am currently rerunning the process with a larger allowed hits and hopefully this will fix it.