thanks a lot, I've been using hash-hash-array-array in order to keep memory use down. I think array access is also faster than hash, so I did this: 
foreach my $rat (@directories) {
      print "Reading Merged_99$rat/bs_seeker-CG.tab ...\n";
      open(FH,"<Merged_99$rat/bs_seeker-CG.tab") or die "cannot read M
+erged_99$rat/bs_seeker-CG.tab: $!";
      while (<FH>) {
         if (/M/) {
            next;
         } elsif ((/^chr(\S+)\s+(\d+)\s+\d+\s+(\d)\.(\d+)\s+(\d+)/) &&
+ ($1 ~~ @CHROMOSOMES) && ($5 >= $MINIMUM_COVERAGE)) {
#chromosome $1, methylated C $2, percent $3.$4 and coverage $5
            $DATA{$1}{$2}[$set][$replicate] = "$3.$4";
         } elsif ((/^chr(\S+)\s+(\d+)\s+\d+\s+(\d)\s+(\d+)/) && ($1 ~~
+ @CHROMOSOMES) && ($4 >= $MINIMUM_COVERAGE)) {
            $DATA{$1}{$2}[$set][$replicate] = $3;
         }
      }
      close FH;
      $replicate++;
   }

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In reply to Re^2: write hash to disk after memory limit by hailholyghost
in thread write hash to disk after memory limit by hailholyghost

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