PAM input format

[dsantesmasses]

Hi,

What is the format for the file containing the pam, eg. PAMs/20bp-NGG-spCas9.txt. I don't seem to find a description of this file.

Thanks!

[ManuelTgn]

Hi @dsantesmasses,

thank you for using CRISPRme in your research!
In order to ensure proper formatting, the PAM file should contain the full PAM sequence and the PAM length, with a space separator between the two. For example, if you're using the spCas9 with a 20bp NGG PAM sequence, your file should look something like this:

NNNNNNNNNNNNNNNNNNNNNGG 3

As an additional resource, I've attached a sample file for the spCas9 NGG PAM, which you can find at the following link: 20bp-NGG-SpCas9.txt. This should give you a good idea of how to format your own PAM file. Let us know if you have any questions!

Best,
Manuel