Extract spacer coordinates about crisprcastyper

[Russel88]

CCTyper 1.6.2 now prints a GFF with all repeat and spacer coordinates

[Russel88]

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

[genomesandMGEs]

Thanks for the detailed explanation Russel!