Hi rambosauce and welcome to the monastery.

I'm a perl novice
I wouldn't have guessed that, your code is quite well written.

To answer your question, here is something you can do: 

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]};
   }    
}

[download]
(Edit: untested for lack of input data)
Now when you are reading the second file, rather than going through all transcripts, you can directly obtain 
my $transcript = $transcripts{$chr}{$strand};
my $start = $transcript->{start};
my $end   = $transcript->{end};
my $info  = $transcript->{info};

[download]
That's assuming that $ref_chr and $ref_strand are a unique pair. If you can have several start/end/info values for a given chr-strand pair, you'll have to use an intermediate array (I didn't want to give the more complex solution if the simple one is enough).

FYI, for debugging you can easer have something like: 

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

[download]
or 
use Data::Dumper;
...
say Dumper \%transcripts;

[download]
The first looks nicer, but Data::Dumper doesn't require an installation.

In reply to Re: How to make a hash to evaluate columns between large datasets by Eily
in thread How to make a hash to evaluate columns between large datasets by rambosauce

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