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Hi,
sometimes aliases are defined in ~/.bash_aliases or ~/.bash_login

Anyway you may set an alias by command line with:

alias <alias>='<command>'

but it's valid only in the current...

Look in /etc/profile.

cd $dpath

c=1

newlist=`echo $list | sed 's/.gz//' `
newnewlist=`echo $newlist | sed 's/.fastq//' `

ls -1 $spath | while read LIST
do
echo "$c"
echo $LIST
c=$(($c+1))
done