I'm looking through some FastQC reports on public data I've downloaded. The reports are mediocre quality, and the trimmers aren't making a difference.
I've discussed this with a colleague, who says that my problem is that many reads are showing overrepresentation in the middle of the sequence. Because the trimmers look for trimming at the beginning and end of sequences, the trimmers or QC tools won't be able to make a difference. My colleague used the phrase "micro-satellites" which will be seen around nucleotides 105-109 with a sharp drop and then rise in %A. I think this will have a very negative effect on the alignment process.
Are there any tools to correct such micro-satellites here? Is this the correct phrase to describe this error? Should I even worry about this?