For a new RNAseq project, I downloaded (foreign but reliable) SRA data of the wildtype control sampe. My FastQC analysis of the data reveals a significant "Illumina Universal Adapter" content, which I´d like to get rid of to have clean reads for later SNP calling analyses. In the FastQC/Configuration directory, I found the text file, that is used by FastQC to identify adapter sequences. The "Illumina Universal Adapter" sequence covers only 12bp.
For my own data's trimming and adapter removal (TruSeq3-PE.fa) I am using Trimmomatic.
Now my question: how do I know which adapters were used/ which adapter sequence I should trim for the downloaded WT SRA data?
Thanks a lot in advance,