Triple or quadruple reads stacked in TRVZ images?

[Jolleboll]

Hello there,

when I make TRVZ images, the 8-10 reads (confirmed with IGV) that span the area are tripled or quadrupled, with mapping differences in the flanking regions. How should I interpret this? Is it a bug or a feature? Enclosing example image below. Note the locations of mismatches etc. to see where the pattern repeats.

Thanks in advance!

Joel

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[egor-dolzhenko]

Thanks for reporting this, Joel! Is it at all possible that TRGT is being run on a BAM file with subreads (instead of a BAM file with consensus HiFi reads)?

Also, would it be permissible for you to share the output of TRGT or a slice of the original BAM file? If yes, please feel free to reach out by email.

Best wishes, Egor