#!/bin/bash
#Copy raw read counts for each sample into one directory
#make new directory containing all raw read counts
mkdir All_Raw_Reads

#loop through sample directories
cat sampleInfo | while read read1 read2 sampleID parentsample nothing;
do
#change into sample directory
cd /scratch/cmp1g20/RMS_resistance_data/LUCILES_DATA/rawdata/"$sampleID"
#copy raw reads for each sample into one directory
cp "$sampleID"_ReadsPerGene.out.tab /scratch/cmp1g20/RMS_resistance_data/LUCILES_DATA/All_Raw_Reads/"$sampleID"_ReadsPerGene.out.tab
cd ../
done

