## example hisat2 command
hisat2 -p 4 --summary-file hisat.summary  -x /home/lakhanp/database/Human/GRCh38p12.gencode30/hisat2_index/GRCh38.primary_assembly.genome.chr.fa -1 /home/lakhanp/analysis/core_projects/43_Ann_ShimLab_RNAseq1/raw_data/Ann/ANN_1_S1_L001_R1_001.fastq.gz -2 /home/lakhanp/analysis/core_projects/43_Ann_ShimLab_RNAseq1/raw_data/Ann/ANN_1_S1_L001_R2_001.fastq.gz | samtools view -bS - | samtools sort  -O bam -o WT_Ctrl_1_hisat2.bam

for i in `cat sample_name.list`
do
cd $i
printf "samtools index %s_hisat2.bam
samtools flagstat %s_hisat2.bam > alignment.stats\n\n" $i $i >> generalJob.sh
cd ..
done

for i in `cat sample_name.list`
do
cd $i
printf "##Run stringtie: just counting the transcripts and no assembly
stringtie %s_hisat2.bam -p 4 -e -B -G /home/lakhanp/database/Human/GRCh38p12.gencode30/annotation/GRCh38p12.gencode.v30.basic.annotation.sorted.gtf -o stringTie_%s/%s.gtf
error_exit \$?\n\n" $i $i $i >> generalJob.sh
cd ..
done