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grybnicky / Spacer2PAM

This repository contains the source code for the R package Spacer2PAM, which is used to guide experimental determination of functional PAM sequences from CRISPR array spacers.
GNU General Public License v3.0
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Comprehensive method #6

Closed ireneortega closed 1 year ago

ireneortega commented 1 year ago

I was wondering how can I use the "Comprehensive" method as described in the publication. Do I have to indicate the different filters criteria so that all together make 256 filters combinations? If so, what is the set of 256 filters you used?

grybnicky commented 1 year ago

Yes, you specify the values for each filter criteria (listed in the publication) in the call with join2PAM. Attached Supplementary File S1 Example Spacer2PAM Script.r.zip is an example script, which is currently being added to the publication (it was meant to, but through a publishing error wasn't). Note the join2PAM call in line 49, which has the comprehensive filter combinations filed in already.

ireneortega commented 1 year ago

Ok, I got the consensus PAM sequence for each prediction out of 256. However, how can I get the logo and score for the consensus PAM sequence after the 256 predicitions in the same way you showed in Figure 2 of your publication? You indicated that the top 25% of high scoring PAM predictions can be used to determine the consensus PAM sequence(s), which I understand, but how can I know the consensus PAM sequence and corresponding score? I mean, how can I convert you Supplementary Table S2 into Figure 2 (supposing Figure 2 is the result of the comprehensive method, which I am not sure about)?