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icebert / eccDNA_RCA_nanopore

eccDNA identification from nanopore long reads of rolling-circle amplicon
MIT License
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code algorithm questions #2

Open 178875 opened 2 years ago

178875 commented 2 years ago

Hello, I have a question while understanding the code, at line 333 of eccDNA_RCA_nanopore.py IMTIRERA8%80U7NG7SVGT14 When looping, when a fragment is unqualified, all subsequent fragments including it will be filtered out, instead of only this one fragment, why is this?

icebert commented 2 years ago

Because the reads are from rolling circle amplification, all the fragments should be consecutive one-by-one. If we drop one middle fragment, we cannot connect the following one with the previous one.

In addition, if all the previous fragments are qualified then one fragment is not qualified, it's high likely due to that branching or template switching happens since this fragment (this is a common phenomenon in rolling circle amplification). So it's better to not make reconstruction after such unqualified fragments.