Primary Considerations for Selecting RNA Sequencing Services
If you're planning to conduct RNA-Seq analysis, you may be considering outsourcing it to a service provider. With many companies now offering RNA Sequencing Services, it can be challenging to select the right one.
In this article, we explain the primary considerations when selecting RNA Sequencing Services. We summarize the key factors you should compare across providers and recommend reviewing them carefully before making your decision.
Overview of the RNA-Seq Workflow at a Service Provider
At most service providers, the general workflow of RNA sequencing services is as follows:
Workflow of RNA Sequencing Services
In general, most RNA sequencing 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 additional 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, you may be able 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 offer volume discounts. Therefore, rather than placing multiple separate orders, it's often better to consolidate your samples and request everything together. Some providers also charge additional fees for delivery or sample submission. In such cases as well, grouping your samples 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.
The sequencing process itself does not take very long, and next-generation sequencers can generate very large amounts of data per run. As a result, providers often batch multiple users' samples together for sequencing. The waiting time required for enough samples to accumulate is one of the main reasons for longer turnaround times. Sequencers like the NovaSeq, which produce especially large data outputs in a single run, can offer lower per-sample costs. However, because they require larger batch sizes, they also tend to have longer turnaround times. If you are submitting many samples, it may be easier to negotiate a shorter turnaround time with the provider.
Many providers also perform quality checks on submitted samples. If any issues are found, resubmission of the samples may be required. For this reason, some providers calculate turnaround time 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 series, are commonly used.
However, some providers offer RNA sequencing services using MGI's DNBSEQ platform. While Illumina has a longer track record and broader adoption, services based on DNBSEQ tend to be more affordable, and several studies have shown that its data quality is comparable to Illumina platforms.
Data Volume
The amount of data generated by sequencing can vary between sequencing runs, but most service providers offer estimates of the expected data output.
It's important to confirm whether the estimated data volume is sufficient for your analysis needs. For standard gene expression analysis in organisms such as humans or mice, around 40 million reads per sample 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 extra fees or may not support certain types of analysis. Even when a provider does offer analysis, the tools used and the output formats can differ greatly between companies, so be sure to confirm that the results you receive will match your specific needs.
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.
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