RNA-Seq analysis
RNA-Seq bioinformatics & analysis
Expert-led transcriptomic analysis — high-fidelity gene expression profiling and deep functional annotation with industry-leading turnaround, managed directly by the computational team.
0–10 days
analysis package turnaround
STAR
high-speed alignment
DESeq2 / EdgeR
differential expression
Any species
custom reference support
Scalable bioinformatics solutions
Tiered analysis models
From rapid automated quantification to a dedicated bioinformatician, tiered models turn transcriptomic data — high-yield, clinical FFPE or ultra-low input — into high-confidence, publication-ready insight.
Standard Analysis
Rapid, automated secondary analysis for high-volume gene expression studies.
- FASTQ-to-counts pipeline
- STAR alignment (BAM)
- Gene-level quantification
Best for high-throughput screening and standard differential expression projects.
Request this serviceAdvanced Analysis
Deep-dive transcriptomic profiling for complex research landscapes.
- Isoform quantification
- Alternative splicing (Sashimi plots)
- Pathway enrichment (GSEA)
Best for mechanism-of-action studies, biomarker discovery and clinical translational research.
Request this serviceCustomized Analysis
Tailored bioinformatics workflows built around your specific project parameters.
- Fusion gene detection
- De novo assembly
- Bespoke visualization for non-model organisms
Best for specialized study designs, unique species and complex genomic data integration.
Request this serviceFTE BioFx Model
Dedicated computational expert support for data-intensive, long-term programs.
- An embedded bioinformatician on your team
- Iterative data mining
- Custom tool development
Best for pharma and biotech teams needing scalable capacity without the overhead of new hires.
Request this serviceThe Gateway advantage
Why choose us for RNA-Seq analysis
Validated gold-standard pipelines
Industry-standard STAR and DESeq2/EdgeR workflows meet the highest bar for peer-reviewed publication.
Workflow & kit agnostic
Standard mRNA, target-depleted total RNA, FFPE and specialized small-RNA preps — all kits and strand-specificity needs supported.
Comprehensive annotation
Every gene enriched with biological context using Ensembl, RefSeq and specialized databases.
Interpretation & visualization
Beyond raw counts — pathway enrichment (GSEA) and custom reports with heatmaps, volcano plots and PCA clustering.
Multi-omics integration ready
Optional services merge transcriptomic data with proteomics, epigenetics or single-cell datasets.
End-to-end transparency
All primary and secondary data — FASTQ, aligned BAM, raw and normalized count matrices — plus publication-ready reports.
Scientist-to-scientist support
Work directly with the computational team to refine parameters or customize figures for specific journals.
Analysis workflow
From raw reads to actionable results
Step 1
Consultation
Define analysis goals — from standard DGE to isoform-level mechanistic studies.
Step 2
Data ingestion
Transfer FASTQ or BAM via secure SFTP — sequencing provider agnostic.
Step 3
Secondary QC
FastQC and MultiQC evaluate depth, base quality and adapter contamination before analysis.
Step 4
Analysis & interpretation
STAR alignment, quantification, DGE and pathway enrichment per package.
Step 5
Delivery & reporting
Full data package plus a detailed PDF report with publication-ready figures.
Beyond the FASTQ
Figures & outputs we deliver
A comprehensive package — raw FASTQ, aligned BAM files, raw and normalized count matrices, and a detailed report with publication-ready figures.
Deliverables include
Volcano plots
Tumor microenvironment analysis
Gene networks
Dot plots
Volcano plots
Tumor microenvironment analysis
Gene networks
Dot plots
Alignment stats
PCA plots
Correlation plots
Heatmaps
Alignment stats
PCA plots
Correlation plots
Heatmaps
Figures & files delivered with every project — hover to pause
Applications
Where this service delivers
Differential gene expression
Quantify transcriptional changes across experimental conditions or drug treatments.
Isoform & splicing analysis
Characterize alternative splicing events and transcript-level variation.
Biomarker discovery
Identify unique gene signatures associated with disease states or therapeutic response.
Pathway & network analysis
Map expression data to biological pathways to uncover systemic insights.
Low-input & single-cell analysis
Extract robust signals from precious clinical specimens and FACS-sorted populations.
FAQs
Plan your project
Resources & insights
Go deeper
Explore related analysis services
More analysis options
Turn RNA into meaningful biological insight
Partner with the network for end-to-end RNA sequencing and bioinformatics.
- Guided study design & platform selection
- Competitive pricing, flexible turnaround
- Integrated bioinformatics & reporting
Ready to launch your study?
Share your samples and goals — a doctoral-level scientist responds within one business day with a study plan and competing blind quotes.
- Expert-guided study design & service matching
- Competitive quotes, adaptable turnaround times
- End-to-end bioinformatics & reporting
- Run by accredited facilities across the nationwide network
Administered by Syntax of Life Private Limited
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