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As mentioned in the title, I want to annotate the N genes in some MAGs, if I can use the ORF predicted from prodigal? And I want to know the difference between the two databases. Before use, are they…
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Hi, I want to run fixstart to start from the coi gene of the mitochondria. I have provided 40 coi genes in nucleotide format with a broad representation from my phylum of interest. On running fixstart…
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Hi some of my runs fail with this error
Traceback (most recent call last):
File "conda/envs/plasx/bin/plasx", line 8, in
sys.exit(run())
File "conda/envs/plasx/lib/python3.8/site-packag…
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Hello I want to build my own database (GTDB + own built MAGs). I used prodigal to convert my nucleotide fasta files to protein fasta files.
As I see prodigal assigns as first column of a fasta heade…
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Thank you for creating this tool! Helps me a lot.
I noticed I was missing this output file when I ran ViralRecall:
*.fasta: The DNA coding sequence of the predicted proteins from Prodigal
Runn…
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I work on Gram-positive actinobacteria, which can frequently encoded alternative starts. I've noticed some genes are annotated with a wrong start (frequently too long to comply with an ATG start inste…
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I have been depending on `titles` [in the Gospel Desk API](https://github.com/gospeldesk/api.gospeldesk.org/blob/d709dc9db7a50656158b392f5a4ed4c887f798c2/app.py#L55), but not all days have at least on…
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Hi,
I'm very interested in using your pipeline but can't get it to work. So far, two different people in my lab have tried to install it and use it on two different computers, and we get the same err…
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Hi,
I am trying to install circlator on our HPC cluster. I am trying to use Singularity and convert the docker image, but I ran into an issue that I have been able to reproduce with the docker ima…
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The default parameter of Prodigal -g is 11 which indicate the stop codons TGA, TAG, and TAA. But what are the other parameters refers to?