echo "wt01_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt01_R1_trm.fastq.gz -2 ../qc/wt01_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt01_trm_k20.bam
echo "KO01_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO01_R1_trm.fastq.gz -2 ../qc/KO01_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO01_trm_k20.bam
echo "KO02_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO02_R1_trm.fastq.gz -2 ../qc/KO02_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO02_trm_k20.bam
echo "KO21_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO21_R1_trm.fastq.gz -2 ../qc/KO21_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO21_trm_k20.bam
echo "KO22_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO22_R1_trm.fastq.gz -2 ../qc/KO22_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO22_trm_k20.bam
echo "KO61_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO61_R1_trm.fastq.gz -2 ../qc/KO61_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO61_trm_k20.bam
echo "KO62_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KO62_R1_trm.fastq.gz -2 ../qc/KO62_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KO62_trm_k20.bam
echo "KOIFN_1_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KOIFN_1_R1_trm.fastq.gz -2 ../qc/KOIFN_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KOIFN_1_trm_k20.bam
echo "KOIFN_2_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KOIFN_2_R1_trm.fastq.gz -2 ../qc/KOIFN_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KOIFN_2_trm_k20.bam
echo "KOIL4_1_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KOIL4_1_R1_trm.fastq.gz -2 ../qc/KOIL4_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KOIL4_1_trm_k20.bam
echo "KOIL4_2_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/KOIL4_2_R1_trm.fastq.gz -2 ../qc/KOIL4_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o KOIL4_2_trm_k20.bam
echo "wt02_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt02_R1_trm.fastq.gz -2 ../qc/wt02_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt02_trm_k20.bam
echo "wt21_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt21_R1_trm.fastq.gz -2 ../qc/wt21_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt21_trm_k20.bam
echo "wt22_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt22_R1_trm.fastq.gz -2 ../qc/wt22_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt22_trm_k20.bam
echo "wt61_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt61_R1_trm.fastq.gz -2 ../qc/wt61_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt61_trm_k20.bam
echo "wt62_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wt62_R1_trm.fastq.gz -2 ../qc/wt62_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wt62_trm_k20.bam
echo "wtIFN_1_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wtIFN_1_R1_trm.fastq.gz -2 ../qc/wtIFN_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wtIFN_1_trm_k20.bam
echo "wtIFN_2_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wtIFN_2_R1_trm.fastq.gz -2 ../qc/wtIFN_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wtIFN_2_trm_k20.bam
echo "wtIL4_1_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wtIL4_1_R1_trm.fastq.gz -2 ../qc/wtIL4_1_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wtIL4_1_trm_k20.bam
echo "wtIL4_2_trm"
/data/results/tools/align/hisat/hisat2-2.2.0/hisat2 -k 20 -p 16 --dta -x /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/hisat/mm10_hisat2 -1 ../qc/wtIL4_2_R1_trm.fastq.gz -2 ../qc/wtIL4_2_R2_trm.fastq.gz | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 16 -o wtIL4_2_trm_k20.bam