Why High-Throughput Sequencing & Bioinformatics Matter for Your CRISPR Screen
CRISPR pooled screens generate massive sequencing datasets that require specialized bioinformatics expertise to extract biological meaning. Our High-Throughput Sequencing and Bioinformatics Analysis Service provides a complete solution for processing, aligning, and interpreting your sequencing data—from raw FASTQ files through to ranked hit lists. Designed for drug discovery teams and translational researchers, the service combines cutting-edge alignment algorithms with robust statistical methods to identify enriched or depleted guide RNAs and prioritize the most promising genetic targets.
We handle the entire bioinformatics pipeline: read trimming, alignment to reference genomes, counting of guide RNA abundance, normalization, and hit-calling. Every step is documented with comprehensive QC reports, and the final deliverables are delivered in standard formats compatible with downstream validation. Whether your screen uses a focused library or genome-wide coverage, we tailor the analysis parameters to your experimental design.
What We Offer
End-to-End Data Processing
From raw sequencing reads to count matrices – we perform adapter trimming, quality filtering, and read alignment using validated bioinformatics pipelines optimized for CRISPR screen data. All steps are fully reproducible and documented.
Robust Hit Identification
Apply best-practice statistical models (e.g., MAGeCK, RRA) to identify significantly enriched or depleted guides and genes. False-discovery rate (FDR) controls and fold-change cutoffs are applied as per your experimental design.
Integrated Functional Interpretation
We connect hit lists to biological context through pathway enrichment, protein–protein interaction networks, and literature mining. Results are compiled in an interactive report that facilitates target prioritization for in vitro and in vivo validation.
How the Service Works
You provide sequencing data (FASTQ files) or raw libraries. We perform initial quality assessment using FastQC and MultiQC to confirm read quality, adapter content, and contamination before proceeding.
Low-quality bases and adapter sequences are trimmed with Cutadapt. The cleaned reads are aligned to your reference genome or library plasmid sequence using a mapper suitable for short-read CRISPR data, such as Bowtie or STAR.
We extract guide RNA sequences from aligned reads and count their abundance per sample. Counts are normalized using median-of-ratios or DESeq2-style scaling to account for sequencing depth and library complexity.
Enrichment or depletion of guides and genes is tested using model-based algorithms (e.g., MAGeCK, RRA). We apply multiple-testing correction and generate ranked hit lists with fold-change, p-value, and FDR metrics.
Top hits are mapped to biological pathways (KEGG, GO) and protein interaction databases. A comprehensive final report includes all analytical steps, QC metrics, hit tables, and visualizations (volcano plots, heatmaps, pathway maps).
Typical Project Deliverables
| Item | Description |
|---|---|
| Raw Sequencing Data | FASTQ files with quality scores (passed QC) |
| Alignment Results | BAM/SAM files with aligned reads, plus mapping statistics |
| Count Matrix | Table of guide RNA or gene counts per sample in CSV/TSV format |
| Hit List | Ranked list of significantly enriched/depleted guides and genes with fold-change and FDR |
| Bioinformatics Report | Interactive PDF or HTML report summarizing all methods, QC, and results |
Service Highlights
Tailored Pipelines
We configure the analysis workflow according to your library design (pooled vs. arrayed, genome-wide vs. focused), sequencing platform, and desired stringency. No one-size-fits-all approach.
Comprehensive Quality Control
Every stage—from raw reads to hit calling—includes detailed QC metrics. You receive clear indicators of data quality, library complexity, and potential batch effects.
Expert Bioinformatics Support
Our team of computational biologists has deep experience in CRISPR screen analysis and can advise on experimental design, normalization strategies, and hit prioritization. We communicate directly with your researchers.
Standardized Deliverables
Results are provided in widely used formats (FASTQ, BAM, CSV, PDF) that can be directly imported into downstream validation workflows or submitted for publication.
Related Resource
Recommended Reading
An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis
View on PubMedReady to Accelerate Your Target Discovery?
Contact our team to discuss your CRISPR screen project and receive a tailored bioinformatics analysis plan. We will review your experimental design, library complexity, and data volume to propose the most suitable analysis scope.