Originally posted by Casey in the old forum on 26.07.2012 - 11:06
I see in the HISTORY.txt of the newest version of Augustus that you've added a min_intron_len parameter for species with introns shorter than 39 bp. I'd like to take advantage of this, but I can't find any documentation of how to use it. Could you tell me how can I change this parameter, or point me to some documentation for it?
min_intron_len for short introns
Moderator: bioinf
Re: min_intron_len for short introns
Originally posted by Mario in the old forum on 26.07.2012 - 11:08
Here is an example for human:
Be aware that the species specific parameters of augustus include a length distribution, so that very short introns
are unlikely or have even probability 0 if they were not represented in the training set. You can have a look at this (and can edit it at will) in the file human_intron_probs.pbl in the section after the
keyword [LENGTH].
Have a look at the comment about the format in the file, e.g.
the 11th number is 1000 * Prob(intron length = 10)
Here is an example for human:
Code: Select all
augustus --species=human --min_intron_len=10 example.faare unlikely or have even probability 0 if they were not represented in the training set. You can have a look at this (and can edit it at will) in the file human_intron_probs.pbl in the section after the
keyword [LENGTH].
Have a look at the comment about the format in the file, e.g.
the 11th number is 1000 * Prob(intron length = 10)