ln -s ../exercise_2/ERR145651_t_oases/merge/transcripts.fa ERR145651_t_oases.fa
ln -s ../exercise_2/ERR145651_t_norm_oases/merge/transcripts.fa ERR145651_t_norm_oases.fa
ln -s ../exercise_3/ERR145651_t_trinity/Trinity.fasta ERR145651_t_trinity.fa
ln -s ../exercise_3/ERR145651_s_trinity/Trinity.fasta ERR145651_s_trinity.fa
ln -s ../exercise_2/ERR145651_t_R1.fastq.gz
ln -s ../exercise_2/ERR145651_t_R2.fastq.gz
ln -s ../exercise_2/ERR145651_t_norm_R1.fastq.gz
ln -s ../exercise_2/ERR145651_t_norm_R2.fastq.gz
ln -s ../exercise_3/ERR145651_s_R1.fastq.gz
ln -s ../exercise_3/ERR145651_s_R2.fastq.gz

foreach asm (ERR145651_t_oases ERR145651_t_norm_oases ERR145651_t_trinity ERR145651_s_trinity)
mkdir $asm; cd $asm; mkdir err_log
qsub -N seqclean -sync y -e err_log -o err_log -b y seqclean ../$asm.fa -o $asm.clean.fa
mv cleaning_1 seqclean
mv *.log *.cidx *.sort seqclean
cd ..
end
foreach asm (ERR145651_t_oases ERR145651_t_norm_oases ERR145651_t_trinity ERR145651_s_trinity)
set run = `echo $asm | sed -e 's/\(.*\)_.*$/\1/'`
cd $asm
qsub -N clean -e err_log -o err_log ../clean.sh $asm $run
cd ..
end