Can this split read into more than 2 subreads? about duplex-tools HOT 10 CLOSED

You might like to checkout the split_on_adapter tool. Guppy can also perform this action as part of basecalling.

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Thanks, I will check this out. :)

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Is it possible to use the assess split on adapter tool when allowing for multiple read splits. as this does not generate a split_multiple_times.pkl file.

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Unfortunately don't have that functionality yet, we could look into getting that working it if would fill a function. Would it be helpful for a use case that you have? Obviously you wouldn't have asked if not, but would be good to know if there's already a way to get the numbers you're looking for. What specifically do you want to check?

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I am currently using the split_on_Adapter to split reads formed from proximity ligation. A bit like the Pore-C library but we have generated this with an internal bridge adapter between each ligation site. I am trying to assess how well it does this for reads that find multiple internal adapters because these are the reads that I am interested in, such as multi-contacts.

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Right, there's a question about whether the multiple adapters come from true contacts, or whether they come from missed open pore between the reads. That's one reason why I'd be careful to not take a count of reads with multiple internal adapters as a given. There should be a fix coming for that, look out for anything in release notes mentioning "twitchy" event detection

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Is this release for duplex_tools or Pore-C?

That's interesting as I am seeing where its splitting reads but when I align them to reference, it appears to be a contiguous and I also cannot see any alignment to my adapter in blastn. Maybe I have to tune the edit distance.

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It should be a generic feature, not in duplex-tools or pore-c specifically, I'd say keep an eye on the nanopore community site. Could be worth trying to tune the edit distance, but most valuable would be to take a look at the raw reads and see if there is any open pore between the reads

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Ah OK. I guess in this case as I have used 1D sequencing adapters I should run duplex_tools split to first use it as intended to separate dsDNA_1-dsDNA_2 ligation events and in silico concatenation.

And then run again with my custom adapters that should be internal.

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Yep, that sounds like a sensible plan. Sorry, was misparsing what you're doing, unlikely that you have issues with missed splits (on your own custom adapters)

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