foreach my $rat (@directories) { print "Reading Merged_99$rat/bs_seeker-CG.tab ...\n"; open(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++; }