Issue with Lighter performance about lighter HOT 5 OPEN

What is the average coverage for these data sets? It looks like the depths of coverage is much thinner than the figures showed before.

from lighter.

All of these have an average coverage across the whole genome of greater than 30 fold (average 55.5).

from lighter.

I just added a "-K" feature, which infers alpha from the total number of bases and genome size(very naive method). And it can take care of the different coverage between samples. Can you give this a try?
If this still have the problem, all the reads may have low quality covering the region miscorrected and Lighter will not store those kmers. If this is the case, you can try the parameter "-noQual".
If this could not solve the problem, I think you can try a more conservative correction parameter by setting "-maxcor" to 2 or even 1.

from lighter.

@flashton2003 did you ever go back and try the auto-alpha mode?

from lighter.

No, I never did :-(

from lighter.