How to Choose an RNA-Seq Service Provider: Key Considerations
If you're planning an RNA-Seq experiment, you may be thinking about outsourcing the work to a sequencing service provider. With so many companies now offering RNA-Seq services, choosing the right one can be difficult.
This article covers the key factors to consider when comparing providers. We recommend reviewing these points carefully before placing an order.
Overview of the RNA-Seq Workflow at a Service Provider
The typical workflow at most RNA-Seq service providers looks like this:
Workflow of RNA Sequencing Services
Most providers accept total RNA samples from the user and then carry out the following steps:
- Library preparation
- Sequencing
- Data analysis
Some providers can also extract RNA from cells or tissues for an additional fee.
Not all providers include data analysis. Some deliver only the raw sequencing output (FASTQ files).
Many providers, however, do offer analysis and typically deliver results as summarized expression tables.
You can often reduce costs by handling library preparation or data analysis yourself.
Pricing
Cost is often the deciding factor, especially when budgets are tight. Some providers offer services starting at around $200 per sample. Providers that perform sequencing overseas tend to have lower prices.
Many providers also offer volume discounts for larger sample batches. Rather than splitting samples across multiple orders, it's usually more cost-effective to submit them all at once. Some providers charge separate fees for shipping or sample submission, which is another reason to consolidate orders and lower the per-sample cost.
Turnaround Time
Turnaround times vary widely between providers, typically ranging from two weeks to three months.
The sequencing itself is relatively fast, but next-generation sequencers produce enormous amounts of data per run. To make efficient use of each run, providers usually batch samples from multiple customers together. The wait for enough samples to fill a run is the main reason turnaround times can be long. High-throughput instruments like the NovaSeq offer lower per-sample costs but require larger batches, which can extend wait times further. If you are submitting a large number of samples, you may have more leverage to negotiate a faster turnaround.
Most providers also perform quality checks on submitted samples. If a sample fails QC, you may need to resubmit it. Because of this, some providers define their turnaround time starting from when QC is complete. It's wise to build extra time into your schedule when planning an order.
Sequencers
Different providers use different sequencing platforms. Illumina instruments, particularly the NovaSeq series, are the most widely used.
Some providers, however, use MGI's DNBSEQ platform. Illumina has a longer track record and broader adoption, but DNBSEQ-based services tend to be more affordable, and multiple studies have shown that DNBSEQ data quality is comparable to that of Illumina.
Data Volume
The exact amount of data produced can vary from run to run, but most providers give an estimate of the expected output per sample.
Make sure the estimated data volume is sufficient for your analysis. For standard gene expression profiling in organisms like human or mouse, approximately 40 million reads per sample is generally adequate.
Data Analysis
Sequencing produces raw data in the form of FASTQ files. Downstream analysis can include gene expression quantification, identification of differentially expressed genes (DEGs), gene ontology (GO) analysis, pathway analysis, and more. Be sure to confirm what is included in the service—some providers charge extra for analysis, and others may not support certain analysis types at all. Even among providers that do offer analysis, the software used and the output formats can differ significantly, so verify that the deliverables will meet your specific needs.
Our RNA-Seq data analysis tool makes it easy for beginners to perform gene expression quantification, DEG identification, GO analysis, and pathway analysis directly from FASTQ files.
RNA-Seq Data Analysis Software
This is an RNA-Seq Data Analysis Software recommended for those who:
✔︎ Seeking to avoid outsourcing or collaboration for RNA-Seq data analysis.
✔︎ Lacking time to learn RNA-Seq data analysis.
✔︎ Frustrated by the complexity of existing tools.
Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.
About the Author
BxINFO LLC
A research support company specializing in bioinformatics.
We provide tools and information to support life science research, with a focus on RNA-Seq analysis.