Augustus
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Gaius-Augustus
Genome annotation with AUGUSTUS
When compiling AUGUSTUS on MacOS with Clang, some warnings are generated.
Instead of hard-coding the include and library paths, pkg-config should be used. For example for SQLite: https://github.com/Gaius-Augustus/Augustus/blob/47189535180344e8aa49731237f35ce30efa8395/src/Makefile#L55-L64 Instead pkg-config could be used: INCL += $(pkg-config --cflags sqlite) LIBS += $(pkg-config...
As the title states, the script for joining Augustus predictions across split jobs does not work if the option "--uniqueGeneId=true" is invoked. This is because of the regexp used to...
I have the full Augustus annotations of a closely relates strain that had been trained through Braker using RNA-seq. Is it possible for me to use the output of that...
Hi, I tried to run Augustus, but got this notification FeatureCollection::esource: invalid source key: E ./bin/augustus: ERROR FeatureCollection::esource: invalid source key: E The script I used is ./bin/augustus --genemodel=partial --protein=on...
Creating directory tmp_jkulsosc/. Error in file /users/gaoxl/soft/miniconda3/bin/fix_in_frame_stop_codon_genes.py at line 225: /users/gaoxl/soft/Augustus-3.3.1-tag1/scripts/gtf2gff.pl is not executable!
When invoked without `--exonhints` or `--nomult`, bam2hints expects reads to be sorted by read name. However, in this case, it only checks that any sort order specified in the BAM...
I am looking for an extrinsic configuration file that supports hints from Proteins (P), EST / cDNA (E), RNA-Seq (W), and PacBio (PB). In the config/extrinsic directory, I can see...
Hi, I'm implementing a long-read-based gene prediction pipeline making use of Augustus/3.2.3. I'm using aln2wig to generate a wig track from the pacbio alignment. The alignment was conducted with BLAT...
Hi, I'm trying to train Augustus for UTRs. I got this as a final result. It looks like the UTR failed. ``` ******* Evaluation of gene prediction ******* ---------------------------------------------\ |...
