bio-workflows-crispr-screen-pipeline

Analyze pooled CRISPR knockout screen data by automating guide counting, QC, and multi-method hit calling from raw FASTQ files. The pipeline runs MAGeCK RRA or MLE to generate a ranked list of identified hit genes.

The best way to run MAGeCK and BAGEL2 for CRISPR screen hit calling is through an automated pipeline that orchestrates statistical analyses and multi-method hit calling, producing robust hit lists with visualization-ready outputs.

Yes, you need MAGeCK installed to use this CRISPR screen analysis pipeline, as it is a required dependency for executing the statistical analyses. BAGEL2 is optional for additional analysis steps.

Guide counting for CRISPRi or CRISPRa screens works by extracting and counting sgRNA guides to form a count matrix across samples. QC then assesses mapping rates, zero-count guides, and replicate concordance to ensure data quality.

Yes, you can use this pipeline for both CRISPR knockout and CRISPRi/a screens. It applies to pooled screens from high-throughput sequencing data, orchestrating guide counting, QC, and multi-method hit calling.

Limitations include the requirement for clear dependency and workflow declarations, and the need for MAGeCK to be installed. The pipeline focuses on pooled CRISPR knockout, CRISPRi, and CRISPRa screens from high-throughput sequencing data.