Ok then you can do it this way: 

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 t
+o see how it looks like

[download]
As you can see, this one is trickier. @{ something } uses "something" as an array ref, and since in this case "something" is a subelement of a structure, perl will create the array for you if it doesn't exist (this is autovivification).

Now you use that like this: 

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

[download]
Can a given line in the second file match several transcripts, or can you stop looking when you have a match?

In reply to Re^3: 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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