Augustus
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Gaius-Augustus
Genome annotation with AUGUSTUS
Dear all, I have found a difference in using split results as an input of join_aug_pred.pl. This was mentioned in #73, but I think this thread couldn't give me a...
Hi, I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. Scallop/StringTie and TransDecoder could predict UTRs but unfortunately, Augustus...
Hi, I used the following commands for Augustus. However, how can I recognise which genes Augustus has predicted as partial or complete? ``` #bam2augustus bam2hints –intronsonly --in=${r1} --out=${r1}.intron-hints.gff bam2wig $r1...
Hi! I am running Augustus/3.3.3 using a hintsfile with a large fasta query (155G) in our HPC system, and the program failed due to memory insufficiency even though I have...
Hi! I was running script bamToWig.py using this following command: > ~/Augustus/scripts/bamToWig.py -b merged.bam -g ../../GCF_002910315.2_ASM291031v2_genomic.fna -o merged.wig but returned this error: > Error in file /home/peiwen/projects/rrg-lough/peiwen/software/Augustus/scripts/bamToWig.py at line 173:...
Hi, I was wondering if there is any multithreading scripts or pipeline in Augustus 3. There was a closed issue regarding the matter, which starts with splitting genome, but I...
Anandkumar Surendrarao wrote on July25th, 2018: In a few cases, I see this in my STDERR file: "augustus: ERROR Invalid block no. in SubstateModel::blockNoOfB"
``` a-posteriori probability of viterbi path ---------------------------------------- a-posteriori probability of correct path 204516 times were the paths equally likely (identical). sorted quotients of the rest: 0 quotients were between 1...
Just to clarify, what species is denominated by "Xipophorus_maculatus"? I would thought it would be the platyfish (_Xiphophorus maculatus_), with a typo in the name, but then the commit for...
Hi, I'm working on training Augustus for a new species by using the alternative codon table 6. I've changed the stop codon probabilities from species.paramaters.cfg file. However, I'm still getting...
