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Dobbs-Lab / GTagHD

A repository for the GTagHD Web Tool
GNU General Public License v3.0
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Program can't handle transcripts in reverse strand well. #6

Open gungne opened 5 years ago

gungne commented 5 years ago

I guess with 5'/3' PAM setting, the position/direction on the cDNA and genome is kind of reversed in the case of transcripts in reverse strand. Might be worth it to just get rid of the 5'/3' setting and specify the input PAM sequence format.

cmmann commented 5 years ago

Thank you for the suggestion - we'll discuss how to approach this for the next update.

The reason it is the way it is now is so that we can have a somewhat "PAM agnostic" approach where as long as the nuclease is SpCas9-like and inducing a DSB 3 bp upstream of the end of the gRNA, the PAM can be any length. However, with all the development/discovery of Cas species with more complicated DSBs, this approach is somewhat outdated.

I'll leave this issue open until we address it in the next update.