I have 50 RNA-Seq samples for a project. FastQC reports different TruSeq Adapter, Indexes (mostly 2, 7,5 and 14) for each of them and also some of them might have llumina Single End PCR Primer 1.
I see very good quality score (>30 for most of reads) but there were fluctuation in K-mer part (just like attached image), between bases 42-50. TruSeq Illumina indexes have 65 bases length however I found only 52 bases in reads. I have 2 question :
1- Should I treat each file bases on their overrepresented sequences? 2- How can I trim TruSeq-Indexes ( just those 52 bases)?