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The gff files I'm seeing contain multiple hits to the same gene, and I'm trying to figure out if they are actual gene duplications or if they are duplicates because of assembly/read issues. For examp…
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Hi, I'm testing prodigal (v2.6.3 with Ubuntu) to find ORF in MAG files. Accroding to the documentation I should have got not only "start_type" but also "stop_type" information. But no such things. I d…
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Hi,
I have been able to run prodigal successfully and generate the gene coordinate, protein translation and nucleotide files. When trying to run the -w option for the summary statistics file my cod…
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I would like to bring up the issue again to include partial genes. See the pull request (#37) from @lguy where he implemented it.
I think it would be good for draft genomes and even more for highly fr…
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pip install worked fine except for the notification that prodigal could not be installed. The notification window offered the option to install it but that only gave another error window with "Error w…
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I would like to propose a new feature: to allow Prokka to be called with the output of Glimmer.
This would cause the Prodigal step to be skipped. Instead, the Glimmer output file would be parsed acco…
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I have attached data from the latest 4 series that are updated:
* Emergence S01E05 - Updated 1 November 2019 15:17
* Treadstone S01E03 - Updated 1 November 2019 11:55
* Prodigal Son S01E06 - Upda…
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Hi Leighton,
I've encountered the above error when running find_differential_primers.py
It seems that one of my input sequences did not return any primers from eprimer3 giving an empty table a…
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I didn't know that prodigal can't handle gzip'ed files, so I ran some genomes through it, and prodigal finished successfully (no errors or warnings). However, the output was:
```
>LZ^S^_2^PRݪ^P`E6…
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Hi guys, hope the week is going well!
As per the title, prodigal v2.6.3 is predicting genes across N stretches even when supplied with the `-m` flag. According to the documentation `-m` should make…