min_intron_len for short introns

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katharina
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min_intron_len for short introns

Post by katharina »

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?
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katharina
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Re: min_intron_len for short introns

Post by katharina »

Originally posted by Mario in the old forum on 26.07.2012 - 11:08

Here is an example for human:

Code: Select all

augustus --species=human --min_intron_len=10 example.fa
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)
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