That worked. I was so close... For dereferencing I had tried (and it obviously failed).

my $transcripts_line = join "\t", @{ $transcripts{$transcript_ip}{$tra
+nscript_id}{@transcripts_columns} };
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So the location of that dereference closing bracket made all the difference. I need to stare at this (and look deeper with print) for a minute or two until it makes sense to me why I should be dereferencing a list from just the first two keys before taking a hash slice of that list with the @transcripts_columns array... That's what it looks like your code is doing to me at first glance anyway, perhaps I'm even interpreting that wrong.

Thanks choroba. I'll upvote tomorrow, I'm out of votes for the day.