learner-long-life
commented
7 months ago we discussed this a few weeks ago. My understanding is we have to trust the Oxford Nanopore hardware that all samples are being collected with the same orientation (5' to 3' for example).
In my opinion, whatever software or algorithms we develop to read alignment or assembly, should proceed given this assumption. If it turns out later to be incorrect, we would detect these "systematic lab" errors faster by having working software and having results for biologists to interpret.
I am a good 90% sure the processes we have to check the inverse and our data backwards for our longest common sub string. As we could have gotten the other half of DNA. I THINK it could have been read in backwards (I am not sure about that though)
I think this prevents making chopping to fixed segments. As, we lose that backwards.. makes things a lot harder. We also don't have a lot of data so, we don't want less.
Lets see if we can find papers and information to confirm or deny that.