PinAPL-Py

!! See the Tutorial (PinAPL-Py Tutorial.pdf) for instructions !!

Experienced users can follow the Quick Start below:

Quick Start

0. Install docker on your machine: https://docs.docker.com/engine/installation/

1. Create a working directory and create both a /Data and /Library subfolder inside it

2. Copy your read files (fastq.gz) to the /Data folder

3. Rename your read files. To be recognized and correctly interpreted, the fastq.gz file names of control replicates need to start with “Control_R1_...”, “Control_R2_....” etc. Similarly, file names of treatment replicates (e.g. treatmentX) need to start with “TreatmentX_R1_...”, “TreatmentX_R2_...” etc. For more information on filename requirements see Section 2 of the tutorial.

4. Copy the library file (.tsv) to the /Library folder. The library file is a tab delimited file of all sgRNAs in the library. Columns should be 1: gene_ID, 2: sgRNA_ID, 3: sequence. If you work with the GECKO_v21 library, you can download this file from https://github.com/LewisLabUCSD/PinAPL-Py

5. Download configuration.yaml from https://github.com/LewisLabUCSD/PinAPL-Py and copy it to the working directory.

6. Edit configuration.yaml

   NOTE: For GECKO_v2 enrichment screens, you can leave everything at default.

7. Dockerfile belongs to v2.9 and can be found in https://hub.docker.com/r/oncogx/pinaplpy_docker

8. Start PinAPL-Py from the working directory using Terminal (Windows: Docker Quickstart Terminal)

   docker run -t -i --name pinaplpy_test -v $PWD:/workingdir oncogx/pinaplpy_docker

9. Run PinAPL-py using python from the workingdirectory.

   python /Scripts/PinALP-py