Is there a way to simply get a list of spacers?

[chahatupreti]

Hello,

I have downloaded CCfinder since I want to run it on hundreds of draft genomes. I am mainly interested in finding the list of spacers in each of them. After running CCfinder and seeing the results, I couldn't find a simple way to get to such a list. In the online version, there is a simple button to download spacers. Is it possible to achieve that in the downloadable version of the software?

I cant find the spacers in either the Crisprs_REPORT.tsv or the CRISPR-Cas_summary.tsv.

For reference, here is the command I am running (on Mac) -

./CRISPRCasFinder.pl -i /path/to/my/input.fa -out /path/to/my/output

[chahatupreti]

Anybody have any ideas?

[dcouvin]

Dear Chahat, Thank you for your message. Sorry for the delayed response due to other ongoing works. You can use the '-keep' option in order to download the spacers corresponding to each analyzed sequence. You will find these results in the 'CRISPRFinderProperties' generated folder. You can also download the repeats. See the user manual for other options. Do not hesitate if you have further questions. Best regards, David

[chahatupreti]

Thank you so much David for the response. I did try to run with the -keep option, but there was no 'CRISPRFinderProperties' folder in the output.

My code was - /.../CRISPRCasFinder.pl -i /.../NC_017316.1.fa -out /.../NC_017316.1 –keep

And the folders in the output are attached as a screenshot. What do you think could be happening?

Thank you!

[chahatupreti]

Actually I then tried to put the -keep option twice as in -keep -keep and that did the trick!

Thank you!

[dcouvin]

Great! You are welcome!