Guide to Choosing RNA-Seq Service Providers: Key Factors for Comparing Companies
If you're planning to conduct RNA-Seq analysis, you may be considering outsourcing it to a service provider. With so many companies offering RNA-Seq services, choosing the right one can be a difficult decision.
In this article, we summarize the key factors to consider when comparing RNA-Seq service providers. We recommend reading it before selecting a provider for your RNA-Seq analysis.
Overview of the RNA-Seq Workflow at a Service Provider
At most service providers, the general workflow of RNA-Seq services is as follows:
Workflow of RNA-Seq Services
In general, most RNA-Seq service providers perform the following steps using total RNA samples provided by the user:
- Library preparation
- Sequencing
- Data analysis
Some providers offer additional services, such as RNA extraction from cells or tissues, for an extra fee.
There are also providers that do not perform data analysis and instead provide only the raw sequencing data (FASTQ files).
Many providers, however, are able to perform data analysis and typically return results in the form of summarized expression tables.
By performing steps like library preparation or data analysis yourself, it may be possible to reduce the overall cost.
Pricing
Pricing is a critical factor, especially when working within a limited budget. Some providers offer services starting at around $200 per sample. In many cases, providers that conduct sequencing overseas tend to offer lower prices.
Additionally, if you have a large number of samples, many providers may offer volume discounts. Therefore, rather than placing multiple separate orders, it's often better to consolidate your samples and request everything at once. Some providers also charge additional fees for delivery or sample submission. In such cases as well, grouping your samples together can help reduce the cost per sample.
Turnaround Time
Turnaround times can vary significantly depending on the provider, typically ranging from two weeks to three months.
While the sequencing process itself does not take very long, next-generation sequencers generate large volumes of data. As a result, providers often batch multiple users' samples together for sequencing. This waiting period for other samples to accumulate is a major reason for longer turnaround times. Sequencers like the NovaSeq, which can generate large amounts of data in a single run, tend to offer lower per-sample costs. However, because they require more samples to be grouped together, they also tend to have longer turnaround times. Given these factors, if you are submitting a large number of samples, it may be easier to negotiate a shorter turnaround time with the provider.
Many providers perform quality checks on the submitted samples, and if any issues are found, resubmission of the samples may be required. Therefore, some providers set the turnaround time starting from the completion of the quality check. It's recommended to plan ahead and allow extra time in your schedule when placing an order.
Sequencers
Each provider may use a different type of sequencer. In many cases, Illumina sequencers, such as the NovaSeq, are commonly used.
However, some providers offer RNA-Seq services using MGI's DNBSEQ platform. While Illumina has a longer track record and more widespread use, services based on DNBSEQ tend to be more affordable, and some studies have shown that the data quality is comparable to that of Illumina platforms.
Data Volume
The amount of data generated by sequencing can vary each time, but most service providers offer an estimate of the expected data output.
It's important to confirm whether the amount of data will be sufficient for the analysis you want to perform. For standard gene expression analysis in organisms like humans or mice, around 40 million reads is generally considered sufficient.
Data Analysis
When sequencing is performed, the raw data is typically provided in the form of FASTQ files. Subsequent data analysis may include gene expression quantification, identification of differentially expressed genes (DEGs), gene ontology (GO) analysis, pathway analysis, and more. It's important to check exactly what is included in the service, as some providers may charge additional fees or may not support certain types of analysis. Even when such analyses are available, the software tools used and the format of the output can vary between providers, so it's essential to confirm whether you'll receive the specific results you need.
Our RNA-Seq data analysis tool allows even beginners to easily perform analyses such as gene expression quantification, identification of DEGs, GO analysis, and pathway analysis directly from FASTQ files.
