adding options to export junction file

diff_exp/geneabundance.sh

@@ -39,8 +39,7 @@ then
 fi
 source /etc/profile.d/modules.sh
 module load subread/1.6.1 stringtie/1.3.2d-intel
-featureCounts -s $stranded -T $SLURM_CPUS_ON_NODE -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
-
+featureCounts -s $stranded -M --fraction -J --ignoreDup -T $SLURM_CPUS_ON_NODE -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
 mkdir ${pair_id}_stringtie
 cd ${pair_id}_stringtie
 stringtie ../${sbam} -p $SLURM_CPUS_ON_NODE -G ../${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt