spike_in_correlation.sh 379 Bytes
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# Spikein data cleanup

for i in $(ls /Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/*counts);
do  raw_fn=$(basename "${i}");
raw_prefix=${raw_fn%.counts};
echo -e "ERCC ID\tCounts" > test.counts;
grep "gSpikein_ERCC" $i >> test.counts;
sed -i '' 's/gSpikein_ERCC/ERCC/' test.counts;
./spike_in_correlation.py -c test.counts -f $raw_fn;
done