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my %transcripts;
{
   open(my $transcripts_fh, "<", $transcripts_qfn)
...
   }    
}
# You should really debug the output at least once with Data::Dumper t
+o see how it looks like

my $transcripts_array = $transcripts{$chr}{$strand}; # might need a be
+tter name
for my $transcript (@$transcripts_array)
{
  my $start = $transcript->{start};
  ...
}