Open aminakur opened 1 year ago
This is somewhat unexpected result from Cactus, but could be some kind of borderline case. Cactus have evolved a lot since we developed Ragout, so it is somewhat hard for me to tell if this is an issue here. Unfortunately, the entire alignment + synteny block generation pipeline is not straightforward to set up. My best advice would be to see if the resulting synteny blocks have good coverage (70-90%+).
I ran maf2synteny on a .maf file produced with Cactus. I thought that .maf files can contain overlapping blocks. Why am I getting this output from maf2synteny and what can I do to fix the problem? P.S. maf2synteny still ran and successfully produced output, but can I trust it given this warning?