Search found 530 matches

by katharina
Thu Nov 19, 2015 2:25 pm
Forum: Predicting Genes with AUGUSTUS
Topic: rna-seq
Replies: 3
Views: 1871

Re: rna-seq

Originally posted by Jammie in the old forum on 11.10.2013 - 04:44 Hi,all : When i ran etraining this program == ./etraining --species=Flower sequence.gb == I get the following error "Segmentation fault" sequence.gb is coming from genebank which file is 72M When i use another small sequen...
by katharina
Thu Nov 19, 2015 2:24 pm
Forum: Predicting Genes with AUGUSTUS
Topic: rna-seq
Replies: 3
Views: 1871

Re: rna-seq

Originally posted by Mario in the old forum on 21.05.2013 - 16:55 Yes, lower intron malus values should lead to fewer predicted unsupported introns. I am giving you an excerpt of an extrinsic file below that I recently used. ass 1 1 0.05 M 1 1e+100 RM 1 1 E 1 1 W 1 1 dss 1 1 0.01 M 1 1e+100 RM 1 1 ...
by katharina
Thu Nov 19, 2015 2:24 pm
Forum: Predicting Genes with AUGUSTUS
Topic: rna-seq
Replies: 3
Views: 1871

rna-seq

Originally posted by Assaf in the old forum on 01.05.2013 - 16:40 Hi all, I see that RNA-Seq supported predictions in augustus become quite accurate by using intron-hints from splice junctions data (similar to what described in http://augustus.gobics.de/binaries/readme.rnaseq.html ). The wig hints ...
by katharina
Thu Nov 19, 2015 2:21 pm
Forum: Training AUGUSTUS
Topic: UTR training sensitivity not improving
Replies: 2
Views: 1776

Re: UTR training sensitivity not improving

Originally posted by Anand KS Rao in the old forum on 19.08.2014 - 06:16 Hi Peter, I just came across your post. I have had similar issues, see my post with values from pre- and post-training (recent post, with same user name). Have you had any resolution to your problem? If yes, could you share he...
by katharina
Thu Nov 19, 2015 2:21 pm
Forum: Training AUGUSTUS
Topic: UTR training sensitivity not improving
Replies: 2
Views: 1776

Re: UTR training sensitivity not improving

Originally posted by PeterM in the old forum on 28.02.2014 - 12:18 The error message probably was because I was accidentally optimizing one parameter set twice. I still have no Idea why the UTR sensitivity never improves after training and why despite not training the UTR (by not setting "--UT...
by katharina
Thu Nov 19, 2015 2:20 pm
Forum: Training AUGUSTUS
Topic: UTR training sensitivity not improving
Replies: 2
Views: 1776

UTR training sensitivity not improving

Originally posted by PeterM in the old forum on 14.02.2014 - 15:30 Hi everyone, I am using optimize_augustus.pl (Augustus V2.7) to train parameters. The option --UTR=on was set. For training I use 1000 manually curated genes with UTR. I am surprised to see that on a test set the sensitivity of the ...
by katharina
Thu Nov 19, 2015 1:50 pm
Forum: Training AUGUSTUS
Topic: How to correct problematic loci and genes removed and filtered out by AUGUSTUS
Replies: 2
Views: 1921

Re: How to correct problematic loci and genes removed and filtered out by AUGUSTUS

Originally posted by Mbandi in the old forum on 15.08.2014 - 10:47

Hi Katharina,
I also get the error messages while running optimize_augustus.pl. This error did not occur when I generated the first try training. --stopCodonExcludedFromCDS is true in *_parameters.cfg.
Thanks,
by katharina
Thu Nov 19, 2015 1:50 pm
Forum: Training AUGUSTUS
Topic: How to correct problematic loci and genes removed and filtered out by AUGUSTUS
Replies: 2
Views: 1921

Re: How to correct problematic loci and genes removed and filtered out by AUGUSTUS

Originally posted by katharina in the old forum on 13.08.2014 - 11:29 I have no experience in using exonerate to generate training genes. I usually use scipio if I need to generate the training genes from proteins and genome. (Scipio is also supported by the autoAug.pl pipeline.) My first idea is t...
by katharina
Thu Nov 19, 2015 1:49 pm
Forum: Training AUGUSTUS
Topic: How to correct problematic loci and genes removed and filtered out by AUGUSTUS
Replies: 2
Views: 1921

How to correct problematic loci and genes removed and filtered out by AUGUSTUS

Originally posted by ThankGod Ebenizer in the old forum on 31.07.2014 - 18:55 Hello Dear, I'm trying to train augustus for my organism (new organism that has not been trained before) using augustus auto training, and I have been running it as so: $ autoAugTrain.pl --useexisting --species=Euglena_gr...
by katharina
Thu Nov 19, 2015 1:47 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Augustus installation error in Mac OSX 10.10.4
Replies: 4
Views: 3294

Re: Augustus installation error in Mac OSX 10.10.4

Originally posted by evoe in the old forum on 12.08.2015 - 06:58

I tried commenting out "# ZIPINPUT = false" line, but I got the same error.
I gave up running Augutus3.1 on Mac OSX 10.10.4, now I utilize it on Biolinux8.
Thank you.
by katharina
Thu Nov 19, 2015 1:47 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Augustus installation error in Mac OSX 10.10.4
Replies: 4
Views: 3294

Re: Augustus installation error in Mac OSX 10.10.4

Originally posted by Lizzy in the old forum on 04.08.2015 - 15:30 oh, I just tried and realized it doesn't work by setting ZIPINPUT = false. It still compiles with ZIPINPUT option turned on. That's probably a bug. Please try commenting out that line in common.mk, so that the line is ignored: "...
by katharina
Thu Nov 19, 2015 1:46 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Augustus installation error in Mac OSX 10.10.4
Replies: 4
Views: 3294

Re: Augustus installation error in Mac OSX 10.10.4

Originally posted by evoe in the old forum on 20.07.2015 - 15:41

Hi Lizzy,

Thank you for your kind advice.

However, I already installed boost and I followed the step you suggested (turn that option off by setting "ZIPINPUT = false" in the file common.mk),
I got the same error message.
by katharina
Thu Nov 19, 2015 1:46 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Augustus installation error in Mac OSX 10.10.4
Replies: 4
Views: 3294

Re: Augustus installation error in Mac OSX 10.10.4

Originally posted by Lizzy in the old forum on 20.07.2015 - 14:13 If you use the DZIPINPUT option you need to install the boost library fist. If you do not use zipped input files I would recommend to turn that option off by setting "ZIPINPUT = false" in the file common.mk and type "m...
by katharina
Thu Nov 19, 2015 1:45 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Augustus installation error in Mac OSX 10.10.4
Replies: 4
Views: 3294

Augustus installation error in Mac OSX 10.10.4

Originally posted by Evoe on 19.07.2015 - 17:12 I have a problem in installing augustus-3.1 on Mac OSX10.10.4. When I execute the Makefile, I got this kind of error message: g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O3 -DZIPINPUT -o genbank.o genbank.cc -I../include In file included from genb...
by katharina
Thu Nov 19, 2015 1:42 pm
Forum: WebAUGUSTUS
Topic: Confused between training input and prediction input
Replies: 1
Views: 2304

Re: Confused between training input and prediction input

In principle, if you don't want to add more extrinsic evidence, and if you don't want to alter prediction options, you don't need to run gene prediction, again. It is possible that WebAUGUSTUS prediction will produce slightly different results. As it is possible that two seemingly identical augustus...
by katharina
Thu Nov 19, 2015 1:40 pm
Forum: WebAUGUSTUS
Topic: Confused between training input and prediction input
Replies: 1
Views: 2304

Confused between training input and prediction input

Originally posted by Chirag Parsania in the old forum on 13.08.2015 - 12:54 Hi, I am using augustus web server to predict genes. I have trained augustus using verified ORFs also provided cDNA sequences while training. As an output of training I got optimised parameter for my gene structure. Along w...
by katharina
Wed Nov 18, 2015 6:57 pm
Forum: Predicting Genes with AUGUSTUS
Topic: mitochondria gene prediction
Replies: 1
Views: 1198

Re: mitochondria gene prediction

Originally posted in the old forum by Katharina on 19.10.2015 - 10:49

You should use a gene prediction tool specialized on mitochondria for mitochondrial genomes.
Katharina
by katharina
Wed Nov 18, 2015 6:56 pm
Forum: Predicting Genes with AUGUSTUS
Topic: mitochondria gene prediction
Replies: 1
Views: 1198

mitochondria gene prediction

Originally posted by Tao Zhu in the old forum on 07.08.2015 - 07:59 It seems as if all the gene predictions made by Augustus are assumed to be nucleus genome. Even when I input sequence of mitochondria genome, it still reports multiple exon-intron structure genes, which is not appropriate in organe...
by katharina
Wed Nov 18, 2015 6:56 pm
Forum: Predicting Genes with AUGUSTUS
Topic: Segmentation violation when Augustus reads in hints.gff
Replies: 1
Views: 9019

Re: Segmentation violation when Augustus reads in hints.gff

Originally posted by Robert Bruccoleri in the old forum on 12.04.2013 - 01:28 I just learned that if I reference the sample extrinsic.cfg file augustus.2.7/config/extrinsic/extrinsic.E.cfg instead of extrinsic.cfg file in the tutorial: [SOURCES] M RM E W exonpart 1 .992 M 1 1e+100 RM 1 1 E 1 1 W 1 ...
by katharina
Wed Nov 18, 2015 6:55 pm
Forum: Predicting Genes with AUGUSTUS
Topic: Segmentation violation when Augustus reads in hints.gff
Replies: 1
Views: 9019

Segmentation violation when Augustus reads in hints.gff

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...