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awk 'NR>3 && $2>500{$2-=100}1' OFS="\t" file

Try:
awk 'NR>3 && $2 > 500{$2-=100}1' file

Try this script: #!/usr/bin/perl
for $f (@ARGV){
open I, "$f";
while (<I>){
chomp;
@F=split / /;
$h="$F[0] $F[1]" if $n==0;
$h.=" $F[2]" if $.==1;
$n++ if $.==1;
...

One more thing... shouldn't there be line like this for entries that are identical in both files:chr1 631246 x xinstead of chr1 631246 x e
chr1 631246 e x?

for i in *.fastq; my_variable=`echo $my_variable$i; done

./bowtie [parameters] index_file ~/infiles/$my_varibale outfile.sam