Smart-seq data, unlike 10X data, is oftentimes deposited in a demultiplexed format, meaning each cell gets one set of FASTQ files. In 10X data, yes, there’s just one set of FASTQ files but somewhere within the FASTQ files is a barcode sequence that can help you resolve each individual cell.
The advantage of Smart-seq is you get better coverage across transcripts (for 10X, you’re only sequencing the 3′ end which can make isoform resolution analysis difficult in many cases). Also Smart-seq sequences fewer cells so each cell can get higher sequencing depth (i.e. more reads per cell). The advantage of 10X is, as you noted, the UMIs.
Smart-seq3 is a newer version of Smart-seq that indeed uses UMIs. Basically, you’re going to have one set of FASTQ files (there’s no demultiplexing) but you can use barcodes to resolve individual cells and some of the reads will contain UMIs and other reads will not contain UMIs. The non-UMI containing reads give you better coverage across transcripts (at the expense of not having UMIs).
“when you are sequencing full-length transcripts having UMIs is really not a factor that changes anything”
This is not really true. The purpose of UMIs is to account for amplification bias. In bulk RNA-seq, amplification bias is not really present but in single-cell RNA seq, it is something to be concerned about because you have lower amounts of starting material (which requires many rounds of PCR, and that’s where amplification bias comes in).
In any case, for S …
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