Could not get same result with example data

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shunohki
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Joined: Fri Jun 15, 2018 10:35 am

Could not get same result with example data

Post by shunohki » Thu Jun 21, 2018 6:58 am

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

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katharina
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Re: Could not get same result with example data

Post by katharina » Sat Jun 23, 2018 4:39 pm

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
Katharina

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