Augustus

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How to improve the acurracy in training?

1

Dear authors, I am trying to train a model for species Thamnophis elegans, but found it very difficult to improve the gene level sensitivity which was always

bioinformaticspcj

Hello, I need to predict strict eucaryotic genes from my genome, for that I use Augustus with training parameters used before and I remove gene predicted when they do not...

StromTroopers

augustus: ERROR Properties::getProperty(): cannot convert value "#" of key "/Constant/opalprob" into double

3

Dear authors: I am using autoAugTrain.pl to train a new model for a reference genome, but I met an error: "augustus: ERROR Properties::getProperty(): cannot convert value "#" of key "/Constant/opalprob"...

bioinformaticspcj

mysqlclient

1

Hello everyone, Thank you for such a useful tool. I have been using it for years, however I recently ran into a compilation problem that I cannot sort out. I...

jdmontenegro

error with fix_in_frame_stop_codon_genes.py while using BRAKER-2.1.5

2

I am using augustus-3.3.3 error is reproducible Traceback (most recent call last): File "/augustus-3.3.3/scripts/fix_in_frame_stop_codon_genes.py", line 737, in for ifs_line in ifs_handle: File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0]...

Aled32

Format .gb for training

2

Hi! I want to train augustus using a .gbff file I downloaded from ncbi https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/611/645/GCF_000611645.1_mono_v1/GCF_000611645.1_mono_v1_genomic.gbff.gz But the command: randomSplit.pl Monoraphidium_neglectum_genomic.gbff 100 fails with "size 100 is greater than the number...

kimnegrette3

format of .gb .gff

2

Hi, I want to annotate a Verticillium Genome via command line. I installed augustus and all neccesary stuff to get it work and tested with the example data -> worked....

ziejan

exon-exon-junctions scripts missing

5

Hi, I follow [Incorporating Illumina RNAseq into AUGUSTUS with Tophat](http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.Tophat). Unfortunately, it requires `intron2exex.pl` which has been replaced by [`getIntrons.pl`](https://github.com/Gaius-Augustus/Augustus/commit/47842adb316b4afc6403cce474e1815f479ac2e6). However, Augustus 3.3.3 does not contain the new script. Where...

mictadlo

This concerns exonpart hints on unknown strand, like this: ``` Scaffold_0 w2h ep 4600 4610 5.400 . . src=W ``` The hint can be counted as supporting a CDS (correctly)...

MarioStanke

Augstus CGP stays empty if sequence file contains "-"

4

I am trying to run Augustus in CGP mode. One "species" contains a "-" in it's name. It looks like Augustus is not parsing this right when reading "speciesfilename". I...

fbemm