AUGUSTUS Forum

Originally posted by Robert Bruccoleri in the old forum on 12.04.2013 - 00:29 I am trying to use Augustus 2.7 to model genes in a novel fungal organism, and I'm getting a segmentation violation when the first hint is being read in. We have a good assembled genome sequence, gene models produced with...

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.

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...

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...

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...

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...

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...

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

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...

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...

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...

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...

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?

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?

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?

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...

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...

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

many thankx

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...

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...