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, how many genes you are expecting expected number of genes to detect, etc. For example, if interested in low abundant transcripts, a higher readsequencing depth (i.e., 5 – 10 million reads per sample) may be beneficial.