How to trim adaptor sequences for NEBNext kit
I have RNA-seq reads produced using NEBNext Multiplex oligos. The fastqc results show overreprsented sequences from Clontech SMART CDS Primer II A, and Clontech Universal Primer Mix Long. These I am guessing are my adaptor sequences, therefore I wish to trim them off using trimmomatic. However, I am not sure which adaptor sequence I should specify for trimmomatic? Would I need to create a new adaptor file with the specified sequences or could I just use a generic adaptor file such as Truseq3? Thanks!
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has anyone use trimmomatic with NEBNext adaptors
Trimming adapter sequence for NEBNext kit