Repeat CT in overrepresented sequences
I'm working on an scRNA-seq project and fastqc keeps identifying overrepresented sequences consisting of C and T.
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
I can’t make sense on where this could come from. Any ideas? Thanks!
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Analeigh •
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Which read is it located in?
fastqcis of limited utility with single cell data (especially 10x).CT-rich regions in introns have been reported before. At what positions in your reads does it appear? How does it affect their mapping to reference?