for file in *ds.*; do cd $file; rm DEIM*; cd ..; done
#288 lieka
for file in *ds.*; do cd $file; gunzip DEP*.gz; cd ..; done
#rmdir tuscias dar
for file in *ds.*; do mkdir ${file:0:4}; done
for file in *ds.*; do mv $file/*.fastq ${file:0:4}; done
for file in ????; do cd $file && cat *.fastq > ${file}.fastq && cd ..; done
for file in ????; do echo -n "${file}, " && grep "@" $file/${file}.fastq | wc -l; done > number_of_reads.csv
#dabar cutadapt (process_reads.sh 134)
for file in ????; do cd $file && cutadapt -a AACTGTAGGCACCATCAAT -g GTTCAGAGTTCTACAGTCCGACGATC -m 18 -q 20 --discard-untrimmed ${file}.fastq > ${file%.fastq}_clipped.fastq && cd ..; done
for file in ????; do cd $file && fastq2fasta.pl ${file}_clipped.fastq > ${file}_reads.fa && collapse_reads_md.pl ${file}_reads.fa seq > ${file}_reads_colapsed.fa && cd ..; done