my %transcripts;
{
   open(my $transcripts_fh, "<", $transcripts_qfn)
      or die("Can't open \"$transcripts_qfn\": $!\n");
   while (<$transcripts_fh>) {
      chomp;
      my @refs = split(/\t/, $_);
      my ($ref_chr, $ref_strand) = @refs[0, 6];
      $transcripts{$ref_chr}{$ref_strand} = {start => $refs[3], end => $refs[4], info => $refs[8]};
   }    
}

##</code><code>##

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

##</code><code>##

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

##</code><code>##

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