is necessary to remove TruSeq index adapter with low percent and present in one read?

Question

[Lila M]

Hi everybody, I have paired end data, after running fastqc I found some over represented sequences from TruSeq Index Adapter (less than 0.6%) but when I've found them, are only present in one read. The adapter content looks perfect. I was wondering if is necessary to remove it when is only present in one read and the % is very low. I will do differential expression analysis and differential exon usage. Assuming that the multiqc report after STAR alignment (and not removing the adpaters) are quite good, do you recommend me to remove them?

Many thanks!

Best

[GenoMax]

I do but some may depend on aligners soft-clipping them at alignment time.