adding updates for rna

alignment/rnaseqalign.sh

@@ -55,9 +55,9 @@ else
     module load hisat2/2.1.0-intel
     if [ $fq1 == $fq2 ]
     then
-	hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --add-chrname --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
+	hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
     else
-	hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --add-chrname --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
+	hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
     fi
     if [[ $umi==1 ]]
     then

diff_exp/geneabundance.sh

@@ -34,7 +34,7 @@ then
     SLURM_CPUS_ON_NODE=1
 fi
 source /etc/profile.d/modules.sh
-module load subread/1.5.0-intel stringtie/1.1.2-intel
+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}
 
 mkdir ${pair_id}_stringtie

variants/germline_vc.sh

@@ -62,7 +62,7 @@ module load python/2.7.x-anaconda picard/2.10.3 samtools/1.6 bedtools/2.26.0 snp
 for i in *.bam; do
     if [[ ! -f ${i}.bai ]]
     then
-	samtools index --threads $SLURM_CPUS_ON_NODE $i
+	samtools index -@ $SLURM_CPUS_ON_NODE $i
     fi
 done