I have prepared ATAC-seq libraries following the Omni-ATAC protocol published earlier this year and despite using the column-based cleanup kit they recommend(Zymo D4013) I observe peaks in my Bioanalyzer traces between 50-70bp that I think correspond to primer contamination. The primers I'm using are Nextera primers(Ad1.x/Ad2.x) that are ~60bp in length and already come with Illumina adapter sequences for sequencing so I'm worried that these small fragments will be overrepresented in sequencing /result in poor data yield. If my library yields are low and I can't do size selection to remove these is it worth it to go ahead and try sequencing these libraries?
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