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If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
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[https://www.biostars.org/p/9559284/][1] you could try this
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it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
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