I have to analyze GSE114327. For that, I use GSE instruction based on the below link:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3139597

In that data processing section has written:

FASTQ reads were subjected to adapter removal (cutadapt) per manufacturer's instructions (NEXTflex Small RNA Sequencing Kit v3).

So, I use cutadapt for trimming. Then

The degenerate sequences (N4) at the 5' and 3' end of the reads were removed

based on the instruction. But I don’t understand that sentence and I don’t know how I can remove degenerate sequence (N4) at the 5' and 3' of the reads.

I appreciate if anybody shares his/her comment with me.