spike_in_correlation.sh 379 Bytes
Newer Older
Venkat Malladi's avatar
Venkat Malladi committed
1 2 3 4 5 6 7 8 9 10
# 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