zcat Gene_Corr8.out | awk '{print $1}' | sort -u | awk '{print $1, NR}' > j1

zcat Gene_Corr8.out | sort | join j1 - | \
awk '{print $3, $0}' | sort | join j1 - | \
awk '{print $3, $4, $1, $2, $6}' | sort -n +1 -n +3 | \
awk '$2<$4 {print $0}' | awk -f pick_largest.awk > big_matrix.in

./big_matrix.pl big_matrix.in big_matrix.png

rm j1 big_matrix.in