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];
      my $values= {start => $refs[3], end => $refs[4], info => $refs[8]};
      push @{ $transcripts{$ref_chr}{$ref_strand} }, $values;
   }    
}
# You should really debug the output at least once with Data::Dumper to see how it looks like