FAQ: How should the adaptor sequences be trimmed?

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