Dear Gene

Question

Can I get long-read RNA sequencing on a tight budget? Long read sequencing is historically costly, but we only have a few samples. Is there a realistic way to try Iso-Seq without a huge upfront cost?

Answer

Yes, SeqCenter can help you capture long-read sequencing data and remain within budget. Historically, leveraging long-read RNA sequencing meant committing to the cost of an entire flowcell, creating a significant barrier to entry for smaller projects. SeqCenter has partnered with PacBio to eliminate this barrier. For a short time, we are running a multiplexed IsoSeq promotion meant to generate meaningful long-read RNA data with no sample minimums. As of April 2026, SeqCenter is offering 5M and 10M IsoSeq read packages starting at just $375 or $700, respectively (compare at $2,519 for a full flowcell from our competitor). You can find further information at our PacBio IsoSeq Service Page.

What does this mean for your research?

For $375, you receive 5 million full-length reads. This provides exceptional depth for most small eukaryotes, including fungi, protists, and select plants or insects with genomes under 150Mbp (million base pairs).

Long reads are fundamentally superior to short reads when it comes to de novo transcriptome characterization. While short-read assemblies collapse haplotype information and rely heavily on reference-based isoform detection, full length reads allow for unambiguous transcript assembly. This enables haplotype phasing of transcripts and de novo detection of isoforms in poorly characterized datasets. Long-read transcript data is also well equipped to provide full-length resolution of highly similar splice variants, an application that is nearly impossible using short reads alone.

Not sure if long-read transcripts are appropriate for your project? It comes down to your primary biological question. If your goal is raw gene counting and differential expression of known targets, short-read RNA sequencing remains the gold standard. However, if your research relies on knowing exactly what is being expressed (i.e. discovering novel isoforms, resolving complex splice variants, or performing true haplotype phasing) long-read sequencing provides the unambiguous structural truth you need.

We can help you match the right read depth and package size to your biological question, just reach out!

Ready to power your next transcriptomics discovery?

Add these foundational services to your cart to get started:

• PacBio IsoSeq Services
• Illumina RNA Sequencing (RNA-Seq)