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In https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md It says: > Explanation of the file format of the extrinsic.cfg file. > The gff/gtf file containint the hints must contain somewhere in the last column an entry...
My genome is small (180 Mb) and haploid. As BRAKER2 evidence I have good mapped RNA seq data from this organism, and ~550 same-species/close-species protein sequences. Formerly I would use...
I'm copying the relevant manual text below for ease of reference. Comments describing my confusion are added in bold in square brackets // ### --UTR=on Generate UTR training examples for...
In an older issue request (https://github.com/Gaius-Augustus/BRAKER/issues/349) i asked about getting different BRAKER output when running the same BRAKER script >1 times. From the reply I learned that older versions of...
The BRAKER manual does not specify. I'm using STAR as the aligner. The Augustus protocol paper (Hoff and Stanke 2018) calls sorting optional (if using the STAR aligner).
I am wondering if this is normal BRAKER2 (v 2.1.4) behavior. I had reason to run it multiple times using the same inputs and parameters (it was run in the...
I know there is a previous bugfix on this #65 , and it was marked a closed issue, but I still see it, using 0.12.7 Here's the test input, a...
gffread v0.12.7 ./gffread -g genome.fasta --add-hasCDS -v -E master5.gff (the input gff has mRNA and CDS features.) running the above only outputs the help file to the screen and: Error:...
I input an unpublished reference assembly to stringtie with the -G option . The reference gtf has no UTR data; the transcript boundaries in every case are coterminous with the...
I realize v3.3 is now three versions old, but thought I would put this on the record anyway. I was invoking our HPC's installed AUGUSTUS 3.3 from a BUSCO config...