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awk '{gene[$2];file[FILENAME];count[$2 FS FILENAME]=$1;}
END { printf "gene"; for (i in file) printf OFS i; printf RS
{for (i in gene )
{ printf i;
...

See man join. With join, you must use flat files, as it seeks in anticipation of Cartesian products. Files need to be header free, delimited and sorted. If this is a many to one or one to one deal (a...