minimal intron length default

Question

minimal intron length default

Closed this issue 6 years ago · 4 comments

Hi,

I want to use Lorean for annotating a plant genome. I am wondering about the --max_intron_length parameter. The default in Lorean is 1000. This seems quite low to me. In gmap, the two corresponding parameters --max-intronlength-middle and --max-intronlength-ends have defaults of 500000 and 10000. Is there a reason for the low default in Lorean? Should I increase this value, e.g. to the gmap default of 500000?

Thank you!
Best,
Chris

Answer 1 · 2019-03-01T13:14:35.000Z

Yes,
we set for fungi which have small introns. you can increase the value as you like

Cheers
Luigi

Answer 2 · 2019-03-01T13:16:49.000Z

Thank you!

Answer 3 · 2019-03-01T13:55:18.000Z

Dear Luigi,

would it be possible that you share the parameters you used for the rice & arabidopsis annotations in the paper?

Best,
Chris

Answer 4 · 2019-03-21T10:04:03.000Z

Are they not in the paper? they should be in a supplementary?