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:
At this time, pgmap is not yet published to PyPI. But can be used following these steps:
First you can clone this repo:
git clone https://github.com/FredHutch/pgmap
To install required dependencies:
pip install -r requirements.txt
Now you can install the package
python3 -m pip install .
You'll need to declare four files (we have example data to work with):
- Two sequencing reads files:
- I1 fastq file
- R1 fastq file
- barcodes path which says which barcodes go to which cells
- pgPEN annotations path (this is included in the package)