#!/bin/bash
#run alignment script

#loop through samples
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 alignment script
cp /scratch/cmp1g20/RMS_resistance_data/LUCILES_DATA/STAR_align_and_count.sh .
#submit alignment script 
sbatch ./STAR_align_and_count.sh
cd ../../
done
