search

CRISPRlab / CRISPRviz

A CRISPR repeat|spacer analysis tool
GNU General Public License v2.0
21 stars 2 forks source link

Counts and types of CRISPR? #3

Closed yjiakang closed 4 years ago

yjiakang commented 4 years ago

Hello Thanks for your wonderful tool, I am little confused that how can I get the counts and types of CRISPR in my genome. Just mannually count according to the web-based graph? Thanks in advance.

mnethery commented 4 years ago

Hello, To get the number of CRISPR loci, you can count the number of .crisprs files in the directory where you ran crisprviz.sh. On the command line, you can use something like: find . -maxdepth 1 -name "*.crisprs" | wc -l

To determine the types of each system you need information about the cas genes, so you need to use a classification tool like CRISPRdisco (https://github.com/CRISPRlab/CRISPRdisco), which output information about each strain's type.