cat >tmp.sh
perl '{print "gene_$_\t".int(rand(1000))foreach 1..100}'
for i in `seq 10`
do
sh tmp.sh >num_$i.txt
done

#!usr/bin/perl -w
use strict;
my @file=glob"*.txt";
my %hash;
for my $file (@file){
        open(FH,"<",$file);
        while(<FH>){
                chomp;
                my @arr=split /\t/,$_;
                $hash{$arr[0]}{$file}=$arr[1];
        }
}
for my $key (keys %hash){
        print $key;
        for my $file (@file){
                print "\t",$hash{$key}{$file};
        }
        print "\n";
}

>shell
awk 'print FLIENAME"\t"$0' *.txt >tmp.txt
>R
data=read.table('tmp.txt',sep = '\t',stringsAsFactors = F)
library(reshape2)
fpkm <- dcast(data,formula = V2~V1)