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Hi, I want to run fixstart to start from the coi gene of the mitochondria. I have provided 40 coi genes in nucleotide format with a broad representation from my phylum of interest. On running fixstart it finds the coi gene (provided) for approx 10% of the input contigs (all contigs are complete mitochondria from within the same phylum and also therefore have coi) before defaulting to prodigal. Basically, I want it to start from the coi gene or nothing, even dropping prodigal if needs be. so questions.
How do I lower the stringency so it finds the coi gene using the coi nt (database) sequences provided (what are good settings)? I have tried an array of --min_id and --mincluster options down to 10 for both with no real improvement (not easy to quantify with an input of 400 mitochondria). I could of course increase the size of the coi database provided but this seems defeatist. Is it not more logical to provide a protein sequence for stringency purposes?
Can prodigal be turned off? or is it possible to provide the program with a choice of mt genes at a later date (most seem to choose coi as a default start gene for mitogenomes)?
cheers
The text was updated successfully, but these errors were encountered:
Replying to myself, and after a bit a playing around, --min_id 25 and --mincluster 20 (default) was the least stringent for my dataset, but not easy to fully establish as results aren't constant. If I execute the same command multiple times the program will give different results. Conclusion is at least that the database needs to be larger... shame!
Hi, I want to run fixstart to start from the coi gene of the mitochondria. I have provided 40 coi genes in nucleotide format with a broad representation from my phylum of interest. On running fixstart it finds the coi gene (provided) for approx 10% of the input contigs (all contigs are complete mitochondria from within the same phylum and also therefore have coi) before defaulting to prodigal. Basically, I want it to start from the coi gene or nothing, even dropping prodigal if needs be. so questions.
cheers
The text was updated successfully, but these errors were encountered: