Lenti-STARR

Software Requirements

• Ubuntu/macOS
• MACS2
• bedtools
• R with installed fitdistrplus package

Running from command line

1. Clone Lenti-STARR GitHub repository

   git clone https://github.com/Barski-lab/Lenti-STARR.git

2. Place sorted and indexed BAM files into two separate folders - folder_A and folder_B, where A is STARRSEQ .bam and B is control plasmid .bam
3. Create a folder for output files

   mkdir results

4. Run process.sh script from the Lenti-STARR repository in the folder where you want the outputs to be saved (a.k.a results)

   cd /absolute/path/to/results
   /absolute/path/to/Lenti-STARR/process.sh /absolute/path/to/folder_A /absolute/path/to/folder_B

5. See outputs saved in the results directory

Using Docker container

1. Clone Lenti-STARR GitHub repository

   git clone https://github.com/Barski-lab/Lenti-STARR.git

2. Place sorted and indexed BAM files into two separate folders - folder_A and folder_B where A is STARRSEQ .bam and B is control plasmid .bam
3. Create a folder for output files

   mkdir results

4. Start process.sh script from the docker container mounting folder_A, folder_B, and results folders as shown below

   docker run --rm -ti -w /tmp/results -v /absolute/path/to/folder_A:/tmp/folder_A -v /absolute/path/to/folder_B:/tmp/folder_B -v /absolute/path/to/results:/tmp/results biowardrobe2/starr:v0.0.1 process.sh /tmp/folder_A /tmp/folder_B

5. See outputs saved in the results directory

Notes:

• /absolute/path/to should be replaced with the real locations on your file system