Search found 530 matches

by katharina
Mon Nov 30, 2015 12:30 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

Re: extract gene sequence from AUGUSTUS predictions

Can you please also post the corresponding excerpt from aaa.gff?
by katharina
Mon Nov 30, 2015 12:27 pm
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 7934

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".
by katharina
Mon Nov 30, 2015 11:03 am
Forum: Training AUGUSTUS
Topic: Some confusions about optimize_augustus.pl
Replies: 2
Views: 2650

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...
by katharina
Fri Nov 20, 2015 1:30 pm
Forum: Predicting Genes with AUGUSTUS
Topic: How to cite
Replies: 1
Views: 2340

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....
by katharina
Fri Nov 20, 2015 1:30 pm
Forum: Predicting Genes with AUGUSTUS
Topic: How to cite
Replies: 1
Views: 2340

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 ...
by katharina
Fri Nov 20, 2015 1:30 pm
Forum: WebAUGUSTUS
Topic: interpretation of AUGUSTUS results
Replies: 1
Views: 2890

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...
by katharina
Fri Nov 20, 2015 1:30 pm
Forum: WebAUGUSTUS
Topic: interpretation of AUGUSTUS results
Replies: 1
Views: 2890

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...
by katharina
Fri Nov 20, 2015 1:29 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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 ...
by katharina
Fri Nov 20, 2015 1:29 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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...
by katharina
Fri Nov 20, 2015 1:28 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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.
by katharina
Fri Nov 20, 2015 1:28 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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?
by katharina
Fri Nov 20, 2015 1:28 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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 ...
by katharina
Fri Nov 20, 2015 1:28 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 7902

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?
by katharina
Fri Nov 20, 2015 1:25 pm
Forum: Predicting Genes with AUGUSTUS
Topic: non-canonical splice site patterns
Replies: 1
Views: 2477

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...
by katharina
Fri Nov 20, 2015 1:25 pm
Forum: Predicting Genes with AUGUSTUS
Topic: non-canonical splice site patterns
Replies: 1
Views: 2477

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...
by katharina
Fri Nov 20, 2015 1:24 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extrinstic.cfg
Replies: 1
Views: 2142

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...
by katharina
Fri Nov 20, 2015 1:24 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extrinstic.cfg
Replies: 1
Views: 2142

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
by katharina
Fri Nov 20, 2015 1:23 pm
Forum: WebAUGUSTUS
Topic: training augustus
Replies: 1
Views: 2298

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=, ......
by katharina
Fri Nov 20, 2015 1:23 pm
Forum: WebAUGUSTUS
Topic: training augustus
Replies: 1
Views: 2298

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
by katharina
Fri Nov 20, 2015 1:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: filterBam execution time
Replies: 7
Views: 5038

Re: filterBam execution time

by -C on 21.12.2012 - 22:50
filterBam background jobs processing
I figured it out. thanks for the response.