Tutorial: How to add a new PAM

A cool feature of AlleleAnalyzer is that you can add a new PAM if, say, you discovered a new type of Cas, or want to use a variety that isn't supported in the software as-is. Here is how you do that - although we always encourage starting an issue and we will work to support widely-used Cas varieties.

1.) Add the PAM site to the PAM_LIST.txt document.

The file CAS_LIST.txt in the scripts/ directory of AlleleAnalyzer centralized all of the PAM site information for each Cas variety analyzed by the tool. To add a new Cas/PAM, just add a new line following the below format where the second line is tab (\t) separated.

# Cpf1, PAM 5' of guides
cpf1 TTTN 5'

2.) Search the reference genome for the PAM(s).

python preprocessing/find_pams_in_reference/pam_pos_genome.py 22 ~/hg38.fa Cpf1 ~/hg38_pams/cpf1

3.) Use AlleleAnalyzer tools with your new PAM!

You should be all set at this point to use AlleleAnalyzer tools with your new PAM/Cas.