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filip-husnik / pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.
GNU General Public License v3.0
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Log file numbers do not match the description. #63

Open Methanoutput opened 2 months ago

Methanoutput commented 2 months ago

I have run pseudofinder with a reference genome from nostoc azollae. In the log file i got

Initial ORFS : 6570 Initial ORFS joined : 1070 Pseudogenes (total) : 4378 Pseudogenes (too short) : 2104 Pseudogenes (fragmented) : 418 Pseudogenes (no predicted ORF) : 1823 Pseudogenes (high dN/dS) : 0 Intact genes: 3726

But if i use the formular that stands below it to calculate my intact genes, i would do:

6570 - 1070 - 2104 - 0 = 3396.

Which does not add up to the 3726 intact genes the log file has calculated. And also intact genes and total pseudogenes are more than Initial ORFS? is this because of Pseudogenes (no predicted ORF)?