How to specify -linearGap

[Morriyaty]

Hi,

When I use chainCleaner, -linearGap must be specified:
loose is chicken/human linear gap costs.
medium is mouse/human linear gap costs.
In example, mm10 and hg38, the linearGap is loose. I can't understand why don't use medium.
But in my research, we only have zoker species. In this case, how to set -linearGap? medium or specify a piecewise linearGap tab delimited file?

Bests,
Yinjia

[MichaelHiller]

UCSC prefers to use medium for closer species comparisons (say within placental mammals).
We prefer loose for all kinds of comparisons, as this gives longer chains that e.g. span larger inversions, and I would recommend this.

Best
Michael
loose is default, so you don't need to change anything.

[Morriyaty]

OK， I got it.

Thanks.