Nanopore sequencing of labelled DNA
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5 months ago

We have DNA which has incorporated fluorescent nucleotide analogues. Questions are:
1- Do fluorophore-labelled nucleotides tend to clog the pores? If this happens, can the data still be used to some extent?
2- What base caller would be recommended?
3- Assuming there's no ready-to-go base caller for our data, are there tutorials/pointers on how to train a base caller?
4- If we are only interested in the lengths of labelled DNA fragments, is there a path to get this info that maybe doesn't involve base calling?

sequencing nanopore • 187 views
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@Jean-Karim this may be best posted on ONTs' nanopore forum (when I last checked it needed an invite to join, in case you don't have an account). Please post the solution here if/when you get one.

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OK. Will do. Thanks.

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I don't really have good answers for the other points, but for question 3 I would suggest having a look at sloika. Do you have an idea about the size of the fluorophores? I know BrdU sequencing is not a problem, but that's not quite the same.

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Thanks for the pointer to sloika.
I don't know the exact size but the molecule is on the order of 1200-1300 Da.

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