Search found 530 matches

by katharina
Wed Nov 18, 2015 6:53 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bonus/malus score
Replies: 1
Views: 1155

Re: bonus/malus score

Originally posted by RS in the old forum on 09.06.2014 - 19:49 Hi, Further to my previous question, given I have derived hints from ESTs/mRNAs, which of the hints should I consider as "E" for the source of hint? I suppose exonpart, intronpart, and CDSpart can have "E". Thank you.
by katharina
Wed Nov 18, 2015 6:53 pm
Forum: Predicting Genes with AUGUSTUS
Topic: bonus/malus score
Replies: 1
Views: 1155

bonus/malus score

Originally posted by RS in the old forum on 09.06.2014 - 18:23 Hi, I have a fungal genome assembly along with hints from ESTs and cDNAs. There is a model available for the same species (Fusarium) which I plan to use for the prediction. Could you suggest appropriate bonus and malus scores for such a...
by katharina
Wed Nov 18, 2015 6:52 pm
Forum: Training AUGUSTUS
Topic: retraining hint parameters
Replies: 1
Views: 1328

Re: retraining hint parameters

Originally posted by mario in the old forum on 08.07.2015 - 11:14 I had implemented procedure a long time ago and changed my viewpoint on this in the meantime. If you just want to annotate a singe or a few genomes I rather recommend to vary the extrinsic.cfg file manually. For example you can creat...
by katharina
Wed Nov 18, 2015 6:51 pm
Forum: Training AUGUSTUS
Topic: retraining hint parameters
Replies: 1
Views: 1328

retraining hint parameters

Originally posted by Damian Kao in the old forum on 08.07.2015 - 10:44 At the end of section5 of the readme, there are some instructions for retraining hint parameters. The warning for the section said it is for internal use. Is this not recommended for end users to run? I've tried running the comm...
by katharina
Wed Nov 18, 2015 6:50 pm
Forum: Predicting Genes with AUGUSTUS
Topic: min_intron_len for short introns
Replies: 1
Views: 2277

Re: min_intron_len for short introns

Originally posted by Mario in the old forum on 26.07.2012 - 11:08 Here is an example for human: 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 proba...
by katharina
Wed Nov 18, 2015 6:50 pm
Forum: Predicting Genes with AUGUSTUS
Topic: min_intron_len for short introns
Replies: 1
Views: 2277

min_intron_len for short introns

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...
by katharina
Wed Nov 18, 2015 6:49 pm
Forum: Predicting Genes with AUGUSTUS
Topic: integrating new evidence
Replies: 3
Views: 1817

Re: integrating new evidence

Originally posted by katharina in the old forum on 21.06.2014 - 15:34

It is possible to provide features of an existing annotation as "manual hints". You might need to tune the parameters in the extrinsic config file, though.
Katharina
by katharina
Wed Nov 18, 2015 6:48 pm
Forum: Predicting Genes with AUGUSTUS
Topic: integrating new evidence
Replies: 3
Views: 1817

Re: integrating new evidence

Originally posted by Sam in the old forum on 19.06.2014 - 21:44 Thanks Katharina! To follow-up, I am working with the maize genome and the gene models provided by Ensembl. Is there a way to supply existing gene models and the new hints and ask Augustus to make corrections (if any) to those gene mod...
by katharina
Wed Nov 18, 2015 6:48 pm
Forum: Predicting Genes with AUGUSTUS
Topic: integrating new evidence
Replies: 3
Views: 1817

Re: integrating new evidence

Originally posted by katharina in the old forum on 05.06.2014 - 18:22 I understand that you already prepared intron hints from both data sources in the correct format. When preparing your peptide hints, pay attention that peptide hints contain strand-information. In contrast to coverage information...
by katharina
Wed Nov 18, 2015 6:47 pm
Forum: Predicting Genes with AUGUSTUS
Topic: integrating new evidence
Replies: 3
Views: 1817

integrating new evidence

Originally posted by RS in the old forum on 05.06.2014 - 01:33 Hi, I have new RNA-Seq and peptide data (as evidence) for maize through intron hints and peptide locations in the genome. Could you tell me the best way to incorporate this and get improved predictions on existing gene models? I am hopi...
by katharina
Wed Nov 18, 2015 6:46 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

Re: autoAug.pl result

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/augustus/binaries/tuto...
by katharina
Wed Nov 18, 2015 6:45 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

Re: autoAug.pl result

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?
by katharina
Wed Nov 18, 2015 6:45 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

Re: autoAug.pl result

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?
by katharina
Wed Nov 18, 2015 6:44 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

Re: autoAug.pl result

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?
by katharina
Wed Nov 18, 2015 6:44 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

Re: autoAug.pl result

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 predictio...
by katharina
Wed Nov 18, 2015 6:43 pm
Forum: Predicting Genes with AUGUSTUS
Topic: autoAug.pl result
Replies: 5
Views: 2419

autoAug.pl result

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 au...
by katharina
Wed Nov 18, 2015 6:42 pm
Forum: Predicting Genes with AUGUSTUS
Topic: measuring accuracy
Replies: 2
Views: 1461

Re: measuring accuracy

Originally posted by Julie in the old forum on 18.06.2012 - 03:03

many thankx
by katharina
Wed Nov 18, 2015 6:41 pm
Forum: Predicting Genes with AUGUSTUS
Topic: measuring accuracy
Replies: 2
Views: 1461

Re: measuring accuracy

Originally posted by Mario in the old forum on 15.06.2012 - 11:08 grep -Pc "\tCDS\t" aug.gff grep -Pc "\tgene\t" aug.gff grep -Pc "\ttranscript\t" aug.gff grep -Pc "\tstart_codon\t" aug.gff grep -Pc "\tstop_codon\t" aug.gff count the number of codin...
by katharina
Wed Nov 18, 2015 6:41 pm
Forum: Predicting Genes with AUGUSTUS
Topic: measuring accuracy
Replies: 2
Views: 1461

measuring accuracy

Originally posted by Julie in the old forum on 15.06.2012 - 04:43 Hi all, I am using augustus with different pipelines to annotate a recently assembled plant genome, and now I would like to compare them. Is there any simple way to calculate some statistics about the annotation process? I would like...
by katharina
Wed Nov 18, 2015 6:40 pm
Forum: Training AUGUSTUS
Topic: augustus training and prediction from scratch
Replies: 3
Views: 2852

Re: augustus training and prediction from scratch

Originally posted by katharina in the old forum on 29.05.2012 - 10:16 PASA will produce training gene structures. Hints are regions in the genome for which you have entrinsic evidence for coding regions. The autoAug pipeline produces such hints form BLAT alignments, not from the PASA assemblies. Th...