Read Length
Read 1: Optimal length is between 50 – 100bp. Read lengths <50bp are not recommended since they can be lost through trimming steps resulting in lower alignment rates. Reads >100bp 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): 12bp to read-out the UMI sequence.
Sequencing Depth
We recommend 3 – 4 million reads per sample, but can vary depending on application, size of reference genome, how many genes you are expecting, etc. For example, if interested in low abundant transcripts, a higher read depth i.e., 5 – 10 million reads per sample may be beneficial.