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nioo-knaw / epiGBS2

This is the epiGBS2 snakemake pipeline as published in a preprint version.
MIT License
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Library structure for epiGBS2 #18

Open BrunoBertolasi opened 1 year ago

BrunoBertolasi commented 1 year ago

Hello Maarten,

I have some questions about library structure in order to be correctly processed by epiGBS2 pipeline (Fig. 1 of the epiGBS2 article).

Taking into the account left adapter (BA-I and BA-II) and right adapter (CO-I and CO-II), must the degenerate bases, in the two strands of the same adapter, be complementary? I mean: if, for example, I choose for a BA-I strand the sequence 5'-...ACT...-3' does the BA-II strand have the sequence 5'-...AGT...-3'?

Comparing the two adapters ligated to the same fragment, must the sequence of degenerate bases in the left adapter be the same of the one in the right adapter?

Thank you in advance for your kind help.

Bruno

MaartenPostuma commented 1 year ago

Hi Bruna, The degenerate bases are used to identify PCR duplicates, and are filtered and trimmed in the first step. So they can be any combination of 3 base pairs, and do not have to be the same for the left and right adapter. Kind regards, Maarten