We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and CRISPR library sequencing coverage across all time points and samples.
It is based off of the original code and research from the Berger Lab stored in this repository: https://github.com/FredHutch/GI_mapping
In order to run this pipeline you will need R and to install the pgmap package and its dependencies. In R you can run this to install the package:
install.packages("remotes")
remotes::install_github("FredHutch/pgmap")
Now you can go to our tutorial to get started!
Follow the steps there that will walk you through the example data. Then you can tailor that tutorial to use your own data.