Comments (3)
CCTyper 1.6.2 now prints a GFF with all repeat and spacer coordinates
from crisprcastyper.
Hey,
I'm glad you like the tool!
Extracting coordinates of all spacers is not that straightforward, unfortunately. The start and end in crisprs_all.tab
refer to start and end of the entire CRISPR array.
If you run cctyper with --keep_tmp
it will produce the raw output from minced in minced.out
; from this file you can extract the positions of all repeats and spacers. The newest version of cctyper also detects CRISPR arrays by BLASTing repeats, and positions of these spacers is not readily obtainable. However, these arrays are somewhat rare (except if you're looking for IV-A3 CRISPRs specifically).
It would probably be a good idea to make cctyper output a gff with all the positions in a standardized way. I'll put that on my to do list.
I'm sorry that I can't provide an easy solution at the moment.
Best,
Jakob
from crisprcastyper.
Thanks for the detailed explanation Russel!
from crisprcastyper.
Related Issues (20)
- Complete genome and draft genome HOT 2
- 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
- Meaning of asterisk at the end of protein sequence HOT 1
- Creating empty files when there's no data HOT 1
- castyping.py having an issue with positional arguments. HOT 2
- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
- (Question) provide GFF file for pre computed gene calls? HOT 5
- XGBoost model incompatible HOT 8
- 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
- error while loading shared libraries: libnsl.so.1
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from crisprcastyper.