autoAug.pl result

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katharina
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autoAug.pl result

Post by katharina »

Originally posted by Cecilia in the old forum on 11.06.2012 - 22:40

After running autoAug.pl pipeline on ESTs/transcript assemblies, I've end up with

* autoAug/results/gbrowse/ and
* autoAug/results/predictions/

I compared gbrowse/augustus.E.gbrowse and predictions/augustus.hints.gff and noticed augustus.E.gbrowse has less number of genes/CDS/etc. Is it a 'filtered' version of augustus.hints.gff? If yes, what's the filtering criteria?
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Re: autoAug.pl result

Post by katharina »

Originally posted by Mario in the old forum on 14.06.2012 - 15:33

augustus.hints.gff is from an intermediate step during training. These predicted genes (only CDS) are used to construct a training set of UTRs. Then augustus is further trained on those UTRs and another "round" of predictions is made.
The files in the gbrowse folder are more important results.
If you got a UTR model, predictions including UTRs will usually be better.
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Re: autoAug.pl result

Post by katharina »

Originally posted by Cecilia in the old forum on 15.06.2012 - 02:25

So the files under gbrowse folder is the final prediction? There is no need to run "augustus --species=MyModel --hintsfile=myESTandTranscripts.hint" after all the rounds of autoAug.pl?
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Re: autoAug.pl result

Post by katharina »

Originally posted by Mario in the old forum on 18.06.2012 - 18:48

You do not need to rerun augustus yourself unless you collect additional evidence.
However, I am not so sure about my previous post anymore. Can you do my the favour of posting the lines with the last gene from each of the two files?
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Re: autoAug.pl result

Post by katharina »

Originally posted by AksR in the old forum on 20.07.2012 - 04:31

Is there a step by step tutorial for creating the training set and using it with Augustus?
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Re: autoAug.pl result

Post by katharina »

Originally posted in the old forum by katharina on 20.07.2012 - 12:56

Basically the the autoAug.pl script can be seen as a tutorial.
For creating training genes from proteins and genome, there is also a tutorial that Mario wrote for a workshop: http://bioinf.uni-greifswald.de/augustu ... /tutorial/
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