Comments (2)
Hi
The default mode is best for when the input fasta contains a single genome, no matter if it's complete or draft. Prodigal meta mode is only for short sequences or fasta files with contigs from different bacteria (e.g. metagenomes). So it sounds like you should just use default mode: cctyper genome.fa my_output.
Cheers,
Jakob
from crisprcastyper.
I see. Thank you very much!
from crisprcastyper.
Related Issues (20)
- FileNotFoundError: blast.tab HOT 3
- A complement to CRISRPRCasFinder or its own thing? HOT 1
- Execution against protein fasta and gff HOT 2
- Different results from CRISPR Cas typer web server and standalone version HOT 5
- Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied HOT 2
- ![image](https://user-images.githubusercontent.com/121949837/212599561-d771b233-4bde-4850-8e5f-98a4164f78cb.png)
- Option to use Prodigal-gv
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- Creating empty files when there's no data HOT 1
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- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
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- If minced detects a CRISPR with N's in the repeat sequence
- (Question) How can I plot svg post-hoc after a run? HOT 1
- ValueError: invalid literal for int() with base 10: 'lengt' HOT 2
- access to sequences that used to geenrate Cas profiles
- access to sequences that used to geenrate Cas profiles HOT 1
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