Tigmint not making cuts about tigmint HOT 3 CLOSED

Hello @elsemikk,

The first thing I would try is to use the tigmint-make Makefile instead of running each command separately (which I think you did based on the commands above?). That would just rule out any possible issues with the commands.

Using a very high span value would actually have the effect of causing no cuts, which I know is a bit counter intuitive. That's because a contig only has the potential to be cut if the molecule/physical coverage reaches the span value at some point on the contig. (That's just because the physical coverage ramps up and down on the ends of the contig, but we don't want to shred all of the contig ends.) So, unless you have a physical coverage of 500000 on some of your contigs, you won't see any cutting.

Let me know if you are still seeing the same issue when using the makefile and a more reasonable range of span values, and we can troubleshoot from there!

Thanks for your interest in Tigmint!
Lauren

from tigmint.

Thank you! I did run it with separate commands before, so I reran it with tigmint-make as you suggested and this time it made several cuts, so it must have been an issue with my commands.

from tigmint.

Excellent! I'm glad that solve the issue :)

from tigmint.