#/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt01_R1_trm.fastq.gz -2 wt01_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt0h1_trm.bam
#mv wt0h1_trm.bam wt01_trm.bam
#/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt01_R1_trm.fastq.gz -2 wt01_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt01_trm.bam

echo "KO01_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO01_R1_trm.fastq.gz -2 KO01_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO01_trm.bam
echo "KO02_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO02_R1_trm.fastq.gz -2 KO02_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO02_trm.bam
echo "KO21_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO21_R1_trm.fastq.gz -2 KO21_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO21_trm.bam
echo "KO22_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO22_R1_trm.fastq.gz -2 KO22_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO22_trm.bam
echo "KO61_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO61_R1_trm.fastq.gz -2 KO61_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO61_trm.bam
echo "KO62_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KO62_R1_trm.fastq.gz -2 KO62_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KO62_trm.bam
echo "KOIFN_1_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KOIFN_1_R1_trm.fastq.gz -2 KOIFN_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KOIFN_1_trm.bam
echo "KOIFN_2_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KOIFN_2_R1_trm.fastq.gz -2 KOIFN_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KOIFN_2_trm.bam
echo "KOIL4_1_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KOIL4_1_R1_trm.fastq.gz -2 KOIL4_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KOIL4_1_trm.bam
echo "KOIL4_2_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 KOIL4_2_R1_trm.fastq.gz -2 KOIL4_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o KOIL4_2_trm.bam
echo "wt02_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt02_R1_trm.fastq.gz -2 wt02_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt02_trm.bam
echo "wt21_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt21_R1_trm.fastq.gz -2 wt21_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt21_trm.bam
echo "wt22_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt22_R1_trm.fastq.gz -2 wt22_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt22_trm.bam
echo "wt61_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt61_R1_trm.fastq.gz -2 wt61_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt61_trm.bam
echo "wt62_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wt62_R1_trm.fastq.gz -2 wt62_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wt62_trm.bam
echo "wtIFN_1_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wtIFN_1_R1_trm.fastq.gz -2 wtIFN_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wtIFN_1_trm.bam
echo "wtIFN_2_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wtIFN_2_R1_trm.fastq.gz -2 wtIFN_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wtIFN_2_trm.bam
echo "wtIL4_1_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wtIL4_1_R1_trm.fastq.gz -2 wtIL4_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wtIL4_1_trm.bam
echo "wtIL4_2_trm"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 18 --dta -x mm9_hisat2 -1 wtIL4_2_R1_trm.fastq.gz -2 wtIL4_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o wtIL4_2_trm.bam