The sequences of our oligos used in the workflow are as follows:
|NEBNext Template Switching Oligo
||GCT AAT CAT TGC AAG CAG TGG TAT CAA CGC AGA GTA CAT rGrGrG|
|NEBNext Single Cell RT Primer||AAG CAG TGG TAT CAA CGC AGA GTA CTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TV|
|NEBNext Single Cell cDNA PCR Primer||AAG CAG TGG TAT CAA CGC AGA GT|
Several trimming tools can be used to trim the reads, which have these sequences on their ends. We recommend Flexbar v3.3.0 or later. Instructions to trim the adaptors using Flexbar can be accessed here: https://github.com/nebiolabs/nebnext-single-cell-rna-seq
The typical read length employed for single cell sequencing is 2x75bp but this can be changed depending on insert size distribution.