3. Read alignment - Bowtie2

#!/bin/bash
#PBS -l nodes=1:ppn=9
#PBS -l walltime=6:00:00

module load Bowtie2/2.4.2-GCC-10.2.0 

inds="Be11 Be12 Be21 Be22 Be3 Be37 Be38 Be4 Be41 Be42 \
H1.2 H1.3 H2.7 H2.8 H3.10 H3.7 M1.7 M3.6 M4.10 M5.2"

for ind in $inds; do \

bowtie2 --end-to-end -p 9 -x /user/gent/427/vsc42733/data/bt_reference/B_ter \
-U /user/gent/427/vsc42733/BumbleBeeData/trimmed/trim_$ind.fq.gz \
-S /user/gent/427/vsc42733/BumbleBeeData/mapped/$ind.bt.output.sam