Hi,
I tried to use AUGUSTUS(3.3) with example data on the following webpage.
http://bioinf.uni-greifswald.de/augustu ... index.html
When I tried "Exercise2 step3. MAKE AN INITIAL TRAINING", I could not get the same result as showing on the webpage.
"$augustus --species=bug genes.gb.test | tee firsttest.out"
The result should be like this
----------------------------------------------------------------------------\
transcript | #pred | #anno | TP | FP | FN | sensitivity | specificity |
----------------------------------------------------------------------------|
gene level | 118 | 100 | 53 | 65 | 47 | 0.53 | 0.449 |
----------------------------------------------------------------------------/
But I got a result like this
----------------------------------------------------------------------------\
transcript | #pred | #anno | TP | FP | FN | sensitivity | specificity |
----------------------------------------------------------------------------|
gene level | 99 | 100 | 0 | 99 | 100 | 0 | 0 |
----------------------------------------------------------------------------/
I also try with my data but I got a similar result (no sensitivity and specificity)
I want to know what is wrong with my commanding or dataset.
Thank you much
Could not get same result with example data
Moderator: bioinf
Re: Could not get same result with example data
This is most commonly observed if the option --stopCodonExcludedFromCDS is set incorrectly (possibly, it has changed in the released parameters since the tutorial was created).
Re-run AUGUSTUS with --stopCodonExcludedFromCDS=true (or false, depending on the current setting in your bug/bug_parameters.cfg file; reverse whatever it says there).
Best,
Katharina
Re-run AUGUSTUS with --stopCodonExcludedFromCDS=true (or false, depending on the current setting in your bug/bug_parameters.cfg file; reverse whatever it says there).
Best,
Katharina