Genome length not within range
Opened this issue · 3 comments
Hi and thanks for the tool.
I have been using staramr on my data but I recently obtaind the follwoing result:
- Genome length is not within the acceptable length range [4000000,6000000]
First, what doesa this mean? and,
Second, should/Can we play around with the default cutoffs?
Best regards,
Joao
Hello Joao,
staramr has, slightly restrictive, defaults for genome size range. I believe it was set originally with the Salmonella genome in mind (~5Mbp). You should adjust the default cutoffs to fit with your specific genome. I would try adjusting the
--genome-size-lower-bound and --genome-size-upper-bound parameters and see if that resolves the isssue.
Good luck
Hi,
Thanks for the reply. Hum...I am setting up the tool to run dynamically so that it can take any microorganism. What would be the implications of creating a higher range (e.g., 1Mbp to 10 Mbp) so that I can provide any prokaryote without having to set the genome upper and lower bounds?
Thanks
I think it's largely there as a check for reasonable genome assembly. I think if you trust the assembly then it's fine.