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?