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Can I use single read sequencing for QuantSeq FFPE?

For QuantSeq FFPE sequencing, we recommend using asymmetrical paired-end sequencing.

Read 1 is generated toward the poly(A) tail and directly corresponds to the mRNA sequence.

Read 2, which is optional, contains the Unique Molecular Identifier (UMI) required for UMI de-duplication.

If single read sequencing is performed, UMI collapsing cannot be applied.


Figure | Sequencing read orientation for QuantSeq FFPE is depicted, where Read 1 reflects the mRNA sequence. Limited paired-end sequencing (Read 2 length: 12 nt) is required for UMI read out (UMIs are located at the beginning of Read 2).

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