FastQC reports in the
overrepresented sequences module a warning for all R2 FASTQ's corresponding to a stretch of >50 G's, amounting to <0.5% and <0.3% of the whole library before and after removing of adapters (TrueSeq Nano), respectively.
Our partner that performed the labwork advised not to concern about this, idicating that it is a known artifact of NovaSeq runs and that their quality checks did not pick up on this.
I would like to get some advice on whether or not I should deal with this warning (i.e. add this GGG...GGG to the adapter file passed to
trimmomatic), or should I just leave it as it is and proceed with the alignments.