AUGUSTUS Forum

Originally posted in the old forum by Vickie on 24.10.2012 - 14:23
Hi!
I have a little problem in Augustus outputs.
Using command line: Augustus generates different prediction outputs.
The output that it generates sometimes, the preferred one : http://en.zimagez.com/zimage/augout1.php
And the another one:
http://en.zimagez.com/zimage/augout2.php
As you can see the same scaffold in the first output contains more predicted "genes", and the second contains only one huge "gene". I always use the same command line, only thing that changes is hints.est.gff file. I often generate new hints file because of getting new transcriptome data.
Maybe you can help me solve this problem?

by Mario on 26.10.2012 - 13:13
I understand the output varies with the hints input file.
It is of couse not possible to diagnose without at least a sample of the input. However, here is my guess:
The big gene could be an effect of a build-in mechanism that tries to predict a single gene covering EST alignments from the same hint group. This would be helpfull, e.g. if you sequenced trancripts from the 5'end and 3'end and know that those two sequences are from the same transcript.
You could post a sample of the hints file so I can have a look at your grouping (grp=... in the last field of the gff).
Mario

by Vickie on 29.10.2012 - 13:36
Different Augustus output using the same command line.
Hi again,
Here is augustus outputs (old and new, scaffold00003):
http://dl.dropbox.com/u/34053418/Augustus_outs.txt
Here is grepped hints for scaffold00003 (old and new):
[[http://dl.dropbox.com/u/34053418/Hints.txt
]]
And here is ungrepped hint group examples (old and new, file start):
http://dl.dropbox.com/u/34053418/Hints_ ... estart.txt
Hope this would be helpful for you.
P.S. For hints file making I used Blat, filterPSL.pl & blat2hints.pl according to this tutorial:
http://bioinf.uni-greifswald.de/augustu ... #prephints

by Vickie on 06.11.2012 - 17:51
I found problem.
UTR was on, and when I turned it off, augustus output format became correct again .