What sequencing read length and read depth are recommended for QuantSeq FFPE?

Read Length

Read 1: Optimal length is between 50 – 100 bp. Read lengths <50 bp are not recommended since they can be lost through trimming steps, resulting in lower alignment rates. Reads >100 bp can be used to increase the number of uniquely mapped reads but may lead to a drop in sequence quality as sequencing will start to read into the poly(A) stretch and adapter sequence.

Read 2 (optional): 12 bp to read-out the UMI sequence.

Sequencing Depth

We recommend 3 – 4 million reads per sample, but this number can vary depending on application, size of reference genome, expected number of genes to detect, etc. For example, if interested in low abundant transcripts, a higher sequencing depth (i.e., 5 – 10 million reads per sample) may be beneficial.