I am using the NextSeq trimming option on cutadapt to remove an over represented (0.117%) sequence in my RNA seq data. This sequence consists of 50 bases of G, which if I am not mistaken represent a lack of signal on the flow cell. I entered 20 into the NextSeq trimming section on Cutadapt (on galaxy) and then ran FastQC on the data. The over represented sequence module now has 1.03% but does not display a sequence. Any help or advice would be much appreciated!
Best wishes, Alysha