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my %transcripts;
{
   open(my $transcripts_fh, "<", $transcripts_qfn)
...
      $transcripts{$ref_chr}{$ref_strand} = {start => $refs[3], end =>
+ $refs[4], info => $refs[8]};
   }    
}

my $transcript = $transcripts{$chr}{$strand};
my $start = $transcript->{start};
my $end   = $transcript->{end};
my $info  = $transcript->{info};

use Data::Dump "pp";
...
say pp \%transcripts; # debug the content of %transcripts

use Data::Dumper;
...
say Dumper \%transcripts;