The Online RNA-Seq Analysis Platform You've Been Searching For

Run your own RNA sequencing analysis with Basepair’s automated alignment, differential expression and pathway pipelines. No bioinformatics or coding experience needed.
Analyze Six Samples For Free

Start Your RNA-Seq Data Analysis With a Single Click

No Code Required

We wanted to make RNA-Seq data analysis so simple that users with no programming  experience  or the patience to wait for days for results  could run Basepair’s platform with ease.

Transparency & Reproducibility

Our audit-ready NGS data analysis platform was designed for reproducibility and transparency  from QC and read charts, to interactive plots ready for publication. All RNA-seq tools used in our pipelines are highly cited and peer-reviewed.

Run 1,000+ Analyses in Parallel

Basepair’s RNA-Seq data analysis software is fast. Our platform has the ability to scale to processs thousands of complex analyses an hour.

 Interactive RNA-Seq Analysis Report Features

All our interactive RNA sequencing analysis pipelines include publication-ready reports, ready for use in research papers or downstream analysis. Below are some of the graphs and figures you’ll find in your interactive report.

Accurate QC Data

All RNA-Seq reports include QC charts, which give you an overview of the quality of your data. To ensure the highest quality output, Basepair checks the raw data and assigns a quality rating. This score reveals any contamination in the input data, as well as base distribution and other useful information.

Detailed Read Counts

Tracking reads is an excellent way to reveal what you’re working with  which data was trimmed, and which data is usable. Together with the QC charts, read counts provide easy-to-read, accurate insight into your raw data.

Expression Count Table

Expression count is the number of reads aligning to the exons of a gene. Your results will include both an expression count chart and table for a practical overview of the metrics for each gene.

Genome Browser

For the genome browser, aligned reads are converted to genome coverage, expressing the number of reads at each position in the genome. This interactive plot provides a birds-eye view of your raw data, without the need to convert files for visualization – Basepair automatically does everything under the hood.

Volcano Plot & Heatmap

The volcano plot is useful for determining the thresholds for making up-regulated and down-regulated genes. A set of filters and p-value sliders allow you to modify the volcano plot and accompanying heatmap on the fly. You can then download high-res images of both for publication or further downstream analysis.

Ready to take your RNA sequencing analysis to the next level?

Try these features for yourself. Inspect finished reports or upload your own RNA-Seq data with our free, no-commitment 14-day trial, and see why some of the world’s top institutions are using Basepair to save thousands of hours on their NGS data analysis.

Basepair Work is in Dozens of Peer-Reviewed Journals

"Fast, excellent and reasonably CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data."

Sharen Mckay

Yale University

"I really like how easy the website is to use. And how quickly the results are generated, including figures. I would have never thought about doing a new analysis like I just did."

Emilie Montenont

NYU Langone Health

"Support answers come fast and are always precise!"


Maria Hollnagel

Ulm University