HI, I have a question here, my reads have over all good per base and per sequence quality but there are three potential problems at the same time after QC. These are per base sequence content (the first 10bp bases are unbalanced), a 50bp overrepresented sequences and Kmer content is bad.
So do I need to remove the first 10bp bases first and then do trim 50bp overrepresented?
I have tried to move remove the first 10bp unbalanced bases and I found the QC did not show overrepresented sequence anymore. However, my Kmer content report looks more mess...
So now, I changed to trim 50bp overrepresent sequence, however, I got a variety of length ( from 0 to 88bp) of reads by using cutadapt software. what I need to do next? continue to trim the first 10bp? or ...?