I performed FastQC on paired end data and performed Trimmomatic trimming of TruSeq3-Pe-2.fa
After trimming, I see that the files fail for the kmer AGATCGG. 0 over-represented sequences were found.
However this kmer is already present in my Trimmomatic adapter!
>PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
What should I do? Since I want to perform assembly next I am worried that further tools like BBDuk given in other threads wil reduce some DNA quality.
After trimming, I see that the files fail for the kmer AGATCGG. 0 over-represented sequences were found.
However this kmer is already present in my Trimmomatic adapter!
>PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
What should I do? Since I want to perform assembly next I am worried that further tools like BBDuk given in other threads wil reduce some DNA quality.
Comment