Search found 531 matches
- Wed Nov 18, 2015 6:40 pm
- Forum: Training AUGUSTUS
- Topic: augustus training and prediction from scratch
- Replies: 3
- Views: 6085
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...
- Wed Nov 18, 2015 6:39 pm
- Forum: Training AUGUSTUS
- Topic: augustus training and prediction from scratch
- Replies: 3
- Views: 6085
Re: augustus training and prediction from scratch
Originally posted by Cecilia in the old forum on 24.05.2012 - 02:36 Thanks Katharina. So my command will become: •autoAug.pl --species=NewSpecies --genome=genome.fa --pasa --cdna=evidence.fa I guess the pasa pipeline will handle the EST/transcript alignments to genome so I'm safe to skip the blat/h...
- Wed Nov 18, 2015 6:39 pm
- Forum: Training AUGUSTUS
- Topic: augustus training and prediction from scratch
- Replies: 3
- Views: 6085
Re: augustus training and prediction from scratch
Originally posted by katharina in the old forum on 23.05.2012 - 23:07 You shouldn't use the trainingset flag if you use cDNA-data. trainingset is used for protein sequences, genbank and gff training gene files, only. The value of maxIntronLen could be estimated if you inspect spliced alignments of ...
- Wed Nov 18, 2015 6:38 pm
- Forum: Training AUGUSTUS
- Topic: augustus training and prediction from scratch
- Replies: 3
- Views: 6085
augustus training and prediction from scratch
Originally posted by Cecilia in the old forum on 23.05.2012 - 21:59 I've got genome.fa, some EST sequences and RNA-Seq data for a species. How to do training and genome annotaion using augustus pipeline? My plan is * De novo assembly of RNA-seq reads and get transcripts.fasta file * cat transcripts...
- Wed Nov 18, 2015 6:37 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: X's in the predicted amino acid sequences
- Replies: 1
- Views: 3686
Re: X's in the predicted amino acid sequences
Originally posted by Mario in the old forum on 04.05.2012 - 12:16 They stem from n's in the genome assembly. On a hard-masked genome or when there are assembly gaps, the genome contains unknown nucleotides (N or n). These are by default considered to be somewhat less likely to be in coding regions,...
- Wed Nov 18, 2015 6:36 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: X's in the predicted amino acid sequences
- Replies: 1
- Views: 3686
X's in the predicted amino acid sequences
Originally posted by Sunghee in the old forum on 04.05.2012 - 12:11
In the output of Augustus I have X's in the amino acid sequences.
E.g. SADXXXXXXXXXXXGELD....
Would you tell me what it is?
In the output of Augustus I have X's in the amino acid sequences.
E.g. SADXXXXXXXXXXXGELD....
Would you tell me what it is?
- Wed Nov 18, 2015 6:35 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: very short introns
- Replies: 3
- Views: 5814
Re: very short introns
Originally posted by Mario in the old forum on 16.04.2012 - 13:50 Yes. In the text file tetrahymena_intron_probs.pbl or whatever it is called for your species edit the section after [LENGTH] which gives the intron length distribution. You can fill in a desired length distribution, e.g. with all zer...
- Wed Nov 18, 2015 6:35 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: very short introns
- Replies: 3
- Views: 5814
Re: very short introns
Originally posted by Olivier in the old forum on 16.04.2012 - 13:49
Is there a way to force augustus to put only introns with length < 100 nt? (like --max_intron_len=100 ?)
Thanks again
Best
Olivier
Is there a way to force augustus to put only introns with length < 100 nt? (like --max_intron_len=100 ?)
Thanks again
Best
Olivier
- Wed Nov 18, 2015 6:34 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: very short introns
- Replies: 3
- Views: 5814
Re: very short introns
Originally posted by Mario in the old forum on 11.04.2012 - 16:18 You can set the minimum intron length like this augustus --species=tetrahymena --min_intron_len=15 example.fa The default is 39bp, which for most species is a safe minimum. It makes sense to not decrease this below the actual minimum...
- Wed Nov 18, 2015 6:34 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: very short introns
- Replies: 3
- Views: 5814
very short introns
Originally posted by Olivier in the old forum on 11.04.2012 - 13:13 Hello, I am trying to use augustus to annotate our genome [...] Apparently you already have trained augustus with Tetrahymena, which is the closest model organism. I have ESTs and I have generated a hint file : scaffold51_5 EST51 e...
- Wed Nov 18, 2015 6:31 pm
- Forum: Welcome to AUGUSTUS Forum!
- Topic: Nettiquette
- Replies: 0
- Views: 29812
Nettiquette
Welcome to the AUGUSTUS Forum! The aim of this forum is to provide a discussion platform for all questions about gene prediction, in particular, about gene prediction with AUGUSTUS. Please adhere to the following rules: Respect: Treat other with respect, as you expect to be treated with respect, yo...