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rraadd88 / beditor

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
GNU General Public License v3.0
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defining custom PAM #11

Closed bioinfo4321 closed 5 years ago

bioinfo4321 commented 5 years ago

Hi, I tried to include a new BE in dbepams.tsv, however the guide selection behavior is somewhat strange. My understanding was that a wider windows achieved by changing distance of mutation (or codon) from PAM should allow for more guides being selected. But I am observing the opposite, very few guides for test2 but a lot more for test1 (see criteria in the link below), everything else is same for the 2 beditor runs. Can you think of a reason that may be happening and how to fix it?

link to see below table as formatted

criteria test1 test2 window start 3 3 window end 15 15 distance of mutation from PAM: minimum 14 10 distance of mutation from PAM: maximum 18 18 distance of codon start from PAM: minimum 14 10 distance of codon start from PAM: maximum 20 20

rraadd88 commented 5 years ago

Hi @bioinfo4321 , As you know, there are many factors involved in the gRNA design. So the number of gRNAs designed would differ in case-by-case manner. I would suggest having a discussion about your case over email (rohan.dandage.1@ulaval.ca) instead. Without the details, I may not be able to give any suggestions. If possible please send me the input files (excluding the confidential info, off-course) by email, I will try my best to offer you suggestion then. Thanks. [closing the issue as this is an issue related to users case.]

bioinfo4321 commented 5 years ago

Sure, I will contact you with specific query, appreciate you looking into it. On my question on input format (input format #10), can you comment if there's is a way to allow any mutation at a given position rather than specifying desired mutation.