SCREENR

This is a tool for parsing CRISPRi/a screens and assigned counts to the provided guides

Installation

```bash

clone repo and install binary

git clone https://github.com/noamteyssier/screenr cd screenr cargo install --path .

validate screenr is in your path

screenr --version

look at help menu

screenr --help ```

Usage

Count mapping for a single sample

```bash

perform count mapping for a single fastq

screenr \ --input data/example/subset0000.fastq.gz \ --names lib1 \ --library data/libraries/CRISPRiv2crop28.all.fasta.gz ```

Count mapping for a single sample writing results to an output file

```bash

perform count mapping for a single fastq

screenr \ --input data/example/subset0000.fastq.gz \ --names lib1 \ --library data/libraries/CRISPRiv2crop28.all.fasta.gz --output lib1.tab ```

Count mapping for multiple samples

bash screenr \ --input data/example/subset0000.fastq.gz data/example/subset0001.fastq.gz data/example/subset0002.fastq.gz \ --names lib1 lib2 lib3 \ --library data/libraries/CRISPRi_v2_crop28.all.fasta.gz

Count mapping for all samples in a directory

bash screenr \ --input data/example/subset00*.fastq.gz \ --names lib{0..10} \ --library data/libraries/CRISPRi_v2_crop28.all.fasta.gz

Count mapping for all fastqs in a directory only using a subset of sgRNAs

bash screenr \ --input data/example/subset00*.fastq.gz \ --names lib{0..10} \ --library data/libraries/CRISPRi_v2_crop28.h1.fasta.gz

Count mapping for all fastqs in a directory using a custom search guide

```bash

default = "GTTTAAGAG"

screenr \ --input data/example/subset00*.fastq.gz \ --names lib{0..10} \ --library data/libraries/CRISPRiv2crop28.h1.fasta.gz --guide GCGCGAA ```