#samtools view data/images/proton/DKlab/orsalia/sortedKo01pos.bam.bam | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-data/images/proton/DKlab/orsalia/sortedKo01pos.sorted

samtools view /data/images/proton/DKlab/orsalia/sortedKo02pos.bam.bam | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKo02pos.sorted


#samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt01pos.bam - | samtools view - | htseq-count   --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt01pos.sorted

samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt02pos.sorted.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt02pos.sorted
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt21pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt21pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt22pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt22pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt61pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt61pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt62pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt62pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwtIFN1pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwtIFN1pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwtIFN2pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwtIFN2pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedwt01IL4pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedwt01IL4pos
samtools sort -n -o data/images/proton/DKlab/orsalia/sortedwt02IL4pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-data/images/proton/DKlab/orsalia/sortedwt02IL4pos
samtools sort -n -o  /data/images/proton/DKlab/orsalia/sortedKO21pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt- /data/images/proton/DKlab/orsalia/sortedKO21pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedKO22pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKO22pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedKo61pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKo61pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedKo62pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKo62pos
samtools sort -n -o /data/images/proton/DKlab/orsalia/sortedKOIFN1pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKOIFN1pos
samtools sort -n -o data/images/proton/DKlab/orsalia/sortedKOIFN2pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKOIFN2pos
samtools sort -n -o data/images/proton/DKlab/orsalia/sortedKo1IL4pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKo1IL4pos
samtools sort -n -o data/images/proton/DKlab/orsalia/sortedKo2IL4pos.bam - | samtools view - | htseq-count  --stranded=no - /data/images/proton/DKlab/orsalia2/stringtie/merged.gtf3  > gene_counts_merged3.txt-sortedKo2IL4pos