python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 6_A11263_ARV_CD4M-ATAC-GSM8224601.end1.fastq.gz 6_A11263_ARV_CD4M-ATAC-GSM8224601.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 6_A11263_ARV_CD4M-ATAC-GSM8224601.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 48_A2P036_ARV_CD8M-ATAC-GSM8224643.end1.fastq.gz 48_A2P036_ARV_CD8M-ATAC-GSM8224643.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 48_A2P036_ARV_CD8M-ATAC-GSM8224643.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 46_A2P036_ARV_CD4M-ATAC-GSM8224641.end1.fastq.gz 46_A2P036_ARV_CD4M-ATAC-GSM8224641.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 46_A2P036_ARV_CD4M-ATAC-GSM8224641.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 45_A2P036_ARV_CD4N-ATAC-GSM8224640.end1.fastq.gz 45_A2P036_ARV_CD4N-ATAC-GSM8224640.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 45_A2P036_ARV_CD4N-ATAC-GSM8224640.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 44_A2P036_SIV_CD8M-ATAC-GSM8224639.end1.fastq.gz 44_A2P036_SIV_CD8M-ATAC-GSM8224639.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 44_A2P036_SIV_CD8M-ATAC-GSM8224639.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 41_A2P036_SIV_CD4N-ATAC-GSM8224636.end1.fastq.gz 41_A2P036_SIV_CD4N-ATAC-GSM8224636.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 41_A2P036_SIV_CD4N-ATAC-GSM8224636.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 37_A2P036_Neg_CD4N-ATAC-GSM8224632.end1.fastq.gz 37_A2P036_Neg_CD4N-ATAC-GSM8224632.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 37_A2P036_Neg_CD4N-ATAC-GSM8224632.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 35_A2P032_ARV_CD8N-ATAC-GSM8224630.end1.fastq.gz 35_A2P032_ARV_CD8N-ATAC-GSM8224630.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 35_A2P032_ARV_CD8N-ATAC-GSM8224630.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 1_A11263_SIV_CD4N-ATAC-GSM8224596.end1.fastq.gz 1_A11263_SIV_CD4N-ATAC-GSM8224596.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 1_A11263_SIV_CD4N-ATAC-GSM8224596.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 30_A2P032_SIV_CD4M-ATAC-GSM8224625.end1.fastq.gz 30_A2P032_SIV_CD4M-ATAC-GSM8224625.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 30_A2P032_SIV_CD4M-ATAC-GSM8224625.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 27_A2P032_Neg_CD8N-ATAC-GSM8224622.end1.fastq.gz 27_A2P032_Neg_CD8N-ATAC-GSM8224622.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 27_A2P032_Neg_CD8N-ATAC-GSM8224622.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 24_A0P031_SIV_CD8M-ATAC-GSM8224619.end1.fastq.gz 24_A0P031_SIV_CD8M-ATAC-GSM8224619.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 24_A0P031_SIV_CD8M-ATAC-GSM8224619.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 18_A0P031_ARV_CD4M-ATAC-GSM8224613.end1.fastq.gz 18_A0P031_ARV_CD4M-ATAC-GSM8224613.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 18_A0P031_ARV_CD4M-ATAC-GSM8224613.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 17_A0P031_ARV_CD4N-ATAC-GSM8224612.end1.fastq.gz 17_A0P031_ARV_CD4N-ATAC-GSM8224612.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 17_A0P031_ARV_CD4N-ATAC-GSM8224612.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 12_A11263_Neg_CD8M-ATAC-GSM8224607.end1.fastq.gz 12_A11263_Neg_CD8M-ATAC-GSM8224607.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 12_A11263_Neg_CD8M-ATAC-GSM8224607.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 10_A11263_Neg_CD4M-ATAC-GSM8224605.end1.fastq.gz 10_A11263_Neg_CD4M-ATAC-GSM8224605.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 10_A11263_Neg_CD4M-ATAC-GSM8224605.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 7_A11263_ARV_CD8N-ATAC-GSM8224602.end1.fastq.gz 7_A11263_ARV_CD8N-ATAC-GSM8224602.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 7_A11263_ARV_CD8N-ATAC-GSM8224602.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 5_A11263_ARV_CD4N-ATAC-GSM8224600.end1.fastq.gz 5_A11263_ARV_CD4N-ATAC-GSM8224600.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 5_A11263_ARV_CD4N-ATAC-GSM8224600.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 3_A11263_SIV_CD8N-ATAC-GSM8224598.end1.fastq.gz 3_A11263_SIV_CD8N-ATAC-GSM8224598.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 3_A11263_SIV_CD8N-ATAC-GSM8224598.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 34_A2P032_ARV_CD4M-ATAC-GSM8224629.end1.fastq.gz 34_A2P032_ARV_CD4M-ATAC-GSM8224629.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 34_A2P032_ARV_CD4M-ATAC-GSM8224629.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 32_A2P032_SIV_CD8M-ATAC-GSM8224627.end1.fastq.gz 32_A2P032_SIV_CD8M-ATAC-GSM8224627.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 32_A2P032_SIV_CD8M-ATAC-GSM8224627.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 26_A2P032_Neg_CD4M-ATAC-GSM8224621.end1.fastq.gz 26_A2P032_Neg_CD4M-ATAC-GSM8224621.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 26_A2P032_Neg_CD4M-ATAC-GSM8224621.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 25_A2P032_Neg_CD4N-ATAC-GSM8224620.end1.fastq.gz 25_A2P032_Neg_CD4N-ATAC-GSM8224620.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 25_A2P032_Neg_CD4N-ATAC-GSM8224620.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 20_A0P031_ARV_CD8M-ATAC-GSM8224615.end1.fastq.gz 20_A0P031_ARV_CD8M-ATAC-GSM8224615.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 20_A0P031_ARV_CD8M-ATAC-GSM8224615.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 19_A0P031_ARV_CD8N-ATAC-GSM8224614.end1.fastq.gz 19_A0P031_ARV_CD8N-ATAC-GSM8224614.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 19_A0P031_ARV_CD8N-ATAC-GSM8224614.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 14_A0P031_Neg_CD4M-ATAC-GSM8224609.end1.fastq.gz 14_A0P031_Neg_CD4M-ATAC-GSM8224609.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 14_A0P031_Neg_CD4M-ATAC-GSM8224609.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 13_A0P031_Neg_CD4N-ATAC-GSM8224608.end1.fastq.gz 13_A0P031_Neg_CD4N-ATAC-GSM8224608.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 13_A0P031_Neg_CD4N-ATAC-GSM8224608.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 11_A11263_Neg_CD8N-ATAC-GSM8224606.end1.fastq.gz 11_A11263_Neg_CD8N-ATAC-GSM8224606.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 11_A11263_Neg_CD8N-ATAC-GSM8224606.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 9_A11263_Neg_CD4N-ATAC-GSM8224604.end1.fastq.gz 9_A11263_Neg_CD4N-ATAC-GSM8224604.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 9_A11263_Neg_CD4N-ATAC-GSM8224604.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 8_A11263_ARV_CD8M-ATAC-GSM8224603.end1.fastq.gz 8_A11263_ARV_CD8M-ATAC-GSM8224603.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 8_A11263_ARV_CD8M-ATAC-GSM8224603.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 47_A2P036_ARV_CD8N-ATAC-GSM8224642.end1.fastq.gz 47_A2P036_ARV_CD8N-ATAC-GSM8224642.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 47_A2P036_ARV_CD8N-ATAC-GSM8224642.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 40_A2P036_Neg_CD8M-ATAC-GSM8224635.end1.fastq.gz 40_A2P036_Neg_CD8M-ATAC-GSM8224635.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 40_A2P036_Neg_CD8M-ATAC-GSM8224635.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 33_A2P032_ARV_CD4N-ATAC-GSM8224628.end1.fastq.gz 33_A2P032_ARV_CD4N-ATAC-GSM8224628.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 33_A2P032_ARV_CD4N-ATAC-GSM8224628.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 31_A2P032_SIV_CD8N-ATAC-GSM8224626.end1.fastq.gz 31_A2P032_SIV_CD8N-ATAC-GSM8224626.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 31_A2P032_SIV_CD8N-ATAC-GSM8224626.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 29_A2P032_SIV_CD4N-ATAC-GSM8224624.end1.fastq.gz 29_A2P032_SIV_CD4N-ATAC-GSM8224624.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 29_A2P032_SIV_CD4N-ATAC-GSM8224624.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 28_A2P032_Neg_CD8M-ATAC-GSM8224623.end1.fastq.gz 28_A2P032_Neg_CD8M-ATAC-GSM8224623.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 28_A2P032_Neg_CD8M-ATAC-GSM8224623.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 23_A0P031_SIV_CD8N-ATAC-GSM8224618.end1.fastq.gz 23_A0P031_SIV_CD8N-ATAC-GSM8224618.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 23_A0P031_SIV_CD8N-ATAC-GSM8224618.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 22_A0P031_SIV_CD4M-ATAC-GSM8224617.end1.fastq.gz 22_A0P031_SIV_CD4M-ATAC-GSM8224617.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 22_A0P031_SIV_CD4M-ATAC-GSM8224617.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 21_A0P031_SIV_CD4N-ATAC-GSM8224616.end1.fastq.gz 21_A0P031_SIV_CD4N-ATAC-GSM8224616.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 21_A0P031_SIV_CD4N-ATAC-GSM8224616.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 16_A0P031_Neg_CD8M-ATAC-GSM8224611.end1.fastq.gz 16_A0P031_Neg_CD8M-ATAC-GSM8224611.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 16_A0P031_Neg_CD8M-ATAC-GSM8224611.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 15_A0P031_Neg_CD8N-ATAC-GSM8224610.end1.fastq.gz 15_A0P031_Neg_CD8N-ATAC-GSM8224610.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 15_A0P031_Neg_CD8N-ATAC-GSM8224610.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 4_A11263_SIV_CD8M-ATAC-GSM8224599.end1.fastq.gz 4_A11263_SIV_CD8M-ATAC-GSM8224599.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 4_A11263_SIV_CD8M-ATAC-GSM8224599.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 43_A2P036_SIV_CD8N-ATAC-GSM8224638.end1.fastq.gz 43_A2P036_SIV_CD8N-ATAC-GSM8224638.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 43_A2P036_SIV_CD8N-ATAC-GSM8224638.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 42_A2P036_SIV_CD4M-ATAC-GSM8224637.end1.fastq.gz 42_A2P036_SIV_CD4M-ATAC-GSM8224637.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 42_A2P036_SIV_CD4M-ATAC-GSM8224637.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 39_A2P036_Neg_CD8N-ATAC-GSM8224634.end1.fastq.gz 39_A2P036_Neg_CD8N-ATAC-GSM8224634.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 39_A2P036_Neg_CD8N-ATAC-GSM8224634.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 38_A2P036_Neg_CD4M-ATAC-GSM8224633.end1.fastq.gz 38_A2P036_Neg_CD4M-ATAC-GSM8224633.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 38_A2P036_Neg_CD4M-ATAC-GSM8224633.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 36_A2P032_ARV_CD8M-ATAC-GSM8224631.end1.fastq.gz 36_A2P032_ARV_CD8M-ATAC-GSM8224631.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 36_A2P032_ARV_CD8M-ATAC-GSM8224631.2x36mers.Macaca_nemestrina-Mnem_1.0.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2_A11263_SIV_CD4M-ATAC-GSM8224597.end1.fastq.gz 2_A11263_SIV_CD4M-ATAC-GSM8224597.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v MT | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_nemestrina-Mnem_1.0/bowtie-indexes/Macaca_nemestrina-Mnem_1.0.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2_A11263_SIV_CD4M-ATAC-GSM8224597.2x36mers.Macaca_nemestrina-Mnem_1.0.unique