Why is per base G-content increasing toward the end of the reads in Novaseq?
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2.2 years ago

Good Day all

We just got our first round of novaseq from a new company, and noticed something we haven't seen before;

An increase in G toward the end of the reads. Is this because of Adaptor Content? We have seen adaptor content increase toward the ends of the reads before but usually not with this increase in G.

G increase

G increase

Any insights will be greatly appreciated Thanks!

sequencing multiqc • 813 views
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In two color chemistry G = No signal. It is possible that you have short inserts and because of the length of sequencing your had adapter read-through and then beyond. Scan/trim the data to see if you have adapter present.

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I think it's more failing elongation, they accumulate in each round so you see an increase. Also R2 will sometimes be a complete G if RT didn't work. I add a poly-G adapter to cutadapt when analyzing NextSeq/NovaSeq

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