Spiked Reads?

Question

[Furor]

Dear all,

as a non-native English speaker, I was wondering what 'spiked' refers to in 'identifying spiked reads'. The context is chimeric sequences created with pyrosequencing.

Do I interpret this as outliers, ambiguous/tricky to annotate, or something else?

Thanks in advance!

[Neilfws]

I think questions like this are important reminders that we are not all native English speakers. Hopefully, no-one has ever spiked your drink :-)

[Furor]

Well, next to the obvious 'physical" meaning of spikes, adding alcohol to one's drink was the other explanation ;), and in fact, is quite close to the answer!

regards

Answer 1

[seidel]

"Spiked" usually means something added at a known concentration. In this case it could be DNA molecules added at a known concentration, so that when they are sequenced, they should yield a known proportion of sequence counts (if added in ratios to each other), or so that one can deduce something about the the absolute number of sequence counts given that you know how much you added. Ambion makes a set of molecules at known concentrations for this purpose. I think there's 92 of them, and they are related to a set of controls also used for microarray standardization.

However, spiked can also mean outliers, like something of unusually high abundance in a data stream. As in, "the signal spiked".

[Neilfws]

The first definition is almost certainly the correct one with respect to this question. Good answer.

[Furor]

Thanks! Things seem so obvious once clarified. Thanks for not taking this too trivial.

Kind regards