If available, I add the evidence, sure.
Maybe you should run both. You need to examine results in a Browser, anyway, and then you can compare: scipio genes, ab initio predictions and predictions with scipio hints.
Search found 531 matches
- Mon Nov 30, 2015 12:46 pm
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21099
- Mon Nov 30, 2015 12:30 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
Can you please also post the corresponding excerpt from aaa.gff?
- Mon Nov 30, 2015 12:27 pm
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21099
Re: One question about the using Scipio to do gene prediction
The second command will not work because the gff file is not in hints format. You can easily convert it, though.
HInts format is described shortly in http://bioinf.uni-greifswald.de/augustu ... README.TXT in the section "USING HINTS".
HInts format is described shortly in http://bioinf.uni-greifswald.de/augustu ... README.TXT in the section "USING HINTS".
- Mon Nov 30, 2015 11:03 am
- Forum: Training AUGUSTUS
- Topic: Some confusions about optimize_augustus.pl
- Replies: 2
- Views: 7311
Re: Some confusions about optimize_augustus.pl
1. I did not set the option --cpus=24, so if I would not set the cpus number, dose the script only use 1 cpu? By default, only 1 CPU is used. 2. As I describe above, The time will be out soon and the optimize_augustus.pl won't be finished, so, do any commands or scripts could continue the unfinishe...
- Fri Nov 20, 2015 1:30 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: How to cite
- Replies: 1
- Views: 7167
Re: How to cite
by Mario on 03.09.2012 - 11:04 For this purpose, please cite this paper. Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics, doi: 10.1093/bioinformatics/btn013 http://bioinformatics....
- Fri Nov 20, 2015 1:30 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: How to cite
- Replies: 1
- Views: 7167
How to cite
Originally posted in the old forum by Julie on 24.08.2012 - 12:09 Hello, I used the RNAseq data to improve the genome annotation (BLAT-based pipeline) as described in http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.Augustus Now I am writing the manuscript and I am not sure how to ...
- Fri Nov 20, 2015 1:30 pm
- Forum: WebAUGUSTUS
- Topic: interpretation of AUGUSTUS results
- Replies: 1
- Views: 8103
Re: interpretation of AUGUSTUS results
by Mario on 04.09.2012 - 15:09 In the 6th column there is a score. In augustus, when sampling is turned on (e.g. --sample=100, which is the default for many species) this is the fraction of times this coding exon was sampled. E.g. in chr1 AUGUSTUS CDS 6661 7008 0.54 - 1 transcript_id "g5.t1&qu...
- Fri Nov 20, 2015 1:30 pm
- Forum: WebAUGUSTUS
- Topic: interpretation of AUGUSTUS results
- Replies: 1
- Views: 8103
interpretation of AUGUSTUS results
Originally posted in the old forum by katharina on 04.09.2012 - 10:24 An augustus training web service user asked the following questions: I just got the AUGUSTUS results, but have a question about the results. In the .gff file, each CDS was shown in one row. What do the numbers in each row mean? W...
- Fri Nov 20, 2015 1:29 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
by katharina on 12.10.2012 - 17:18 I give you an example that I recently executed: augustus --species=some_species --exonnames=on --codingseq=on protein=on genome.fa > aug.out getAnnoFasta.pl --seqfile=genome.fa aug.out The latter command gave me the following files: aug.cdsexons # contains coding ...
- Fri Nov 20, 2015 1:29 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
by Tom on 12.10.2012 - 15:31 I tried running Augustus with --codingseq=1 and then ran getAnnoFasta.pl on the resulting gff file, but seemed to get the same results as without the --codingseq=1 (i.e. I get the exons but not the entire gene nucleotide sequence with introns). Can you clarify more plea...
- Fri Nov 20, 2015 1:28 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
by katharina on 23.05.2012 - 22:51
Not that I am aware of it. You'd either have to google a bit or write that script yourself, I guess.
Not that I am aware of it. You'd either have to google a bit or write that script yourself, I guess.
- Fri Nov 20, 2015 1:28 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
by Cecilia on 23.05.2012 - 21:30
What if I finished augustus prediction without --codingseq=1 and --protein=1? Is there a script to extract gene sequences from the gff3 and genome fasta file?
What if I finished augustus prediction without --codingseq=1 and --protein=1? Is there a script to extract gene sequences from the gff3 and genome fasta file?
- Fri Nov 20, 2015 1:28 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
Re: extract gene sequence from AUGUSTUS predictions
by Mario on 15.03.2012 - 10:59 1. Run augustus with --codingseq=1 (and with --protein=1 if you like the amino acid sequence as well). 2. Extract the sequences from the comments in the resulting gff with getAnnoFasta.pl on the resulting gff file. This script also allows you to retrieve the complete ...
- Fri Nov 20, 2015 1:28 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21096
extract gene sequence from AUGUSTUS predictions
Originally posted in the old forum by Matthew on 15.03.2012 - 10:55
Is there a best way to extract the gene nucleotide sequence from the GFF3 output of Augustus?
Is there a best way to extract the gene nucleotide sequence from the GFF3 output of Augustus?
- Fri Nov 20, 2015 1:25 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: non-canonical splice site patterns
- Replies: 1
- Views: 7580
Re: non-canonical splice site patterns
by Mario on 26.10.2012 - 12:58 The option --allow_hinted_splicesites=gttg,gccg allows Augustus to predict these introns in addition to the GT-AG and GC-AG introns that are allowed by default. However, it will not predict these ab initio only. It will predict only those non-standard introns that are...
- Fri Nov 20, 2015 1:25 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: non-canonical splice site patterns
- Replies: 1
- Views: 7580
non-canonical splice site patterns
Originally posted in the old forum by Bram on 26.10.2012 - 12:56 I would like to adopt Augustus into my prediction pipeline but I need to inquire into one issue: Can Augustus handle non-canonical splice sites except (except for AT-AC)? The species I work on have GT-TG, GC-CG,... and more. If I prov...
- Fri Nov 20, 2015 1:24 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extrinstic.cfg
- Replies: 1
- Views: 6774
Re: extrinstic.cfg
by katharina on 29.10.2012 - 12:34 The format of the extrinsic.cfg file is explained for example at http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.GSNAP in section 6.1 We do not provide an automated protocol for adjusting those parameters to the specific needs of a par...
- Fri Nov 20, 2015 1:24 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extrinstic.cfg
- Replies: 1
- Views: 6774
extrinstic.cfg
Originally posted in the old forum by Anna on 29.10.2012 - 11:16
Could you, please, explain how could I adjust the parameters in extrinstic.cfg file?
Best, Anna
Could you, please, explain how could I adjust the parameters in extrinstic.cfg file?
Best, Anna
- Fri Nov 20, 2015 1:23 pm
- Forum: WebAUGUSTUS
- Topic: training augustus
- Replies: 1
- Views: 6719
Re: training augustus
by katharina on 29.10.2012 - 12:30 There is principal difference in the formats of hints and training gene structures: Hints file for AUGUSTUS contain a number of features in column 3 (e.g. CDSpart, intron, exonpart, exon, CDS, ...), and specific tags in the last column (e.g. grp=, mult=, pri=, ......
- Fri Nov 20, 2015 1:23 pm
- Forum: WebAUGUSTUS
- Topic: training augustus
- Replies: 1
- Views: 6719
training augustus
Originally posted in the old forum by Anna on 29.10.2012 - 11:13 Could I use hints from RNA-seq, hints from transcriptome contigst and hints from closely related specie to train Augustus? If not, could I skip pasa assembly step and use assembled transcriptome contigs for training? Greetings, Anna