python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_WT_Rep2_ATAC-seq-GSM3743883.end1.fastq.gz Day3_WT_Rep2_ATAC-seq-GSM3743883.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_WT_Rep2_ATAC-seq-GSM3743883.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_WT_Rep2_ATAC-seq-GSM3743883.end1.fastq.gz Day3_WT_Rep2_ATAC-seq-GSM3743883.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_WT_Rep2_ATAC-seq-GSM3743883.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_WT_Rep1_ATAC-seq-GSM3743882.end1.fastq.gz Day3_WT_Rep1_ATAC-seq-GSM3743882.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_WT_Rep1_ATAC-seq-GSM3743882.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_WT_Rep1_ATAC-seq-GSM3743882.end1.fastq.gz Day3_WT_Rep1_ATAC-seq-GSM3743882.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_WT_Rep1_ATAC-seq-GSM3743882.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_HD_Rep2_ATAC-seq-GSM3743881.end1.fastq.gz Day3_HD_Rep2_ATAC-seq-GSM3743881.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_HD_Rep2_ATAC-seq-GSM3743881.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_HD_Rep2_ATAC-seq-GSM3743881.end1.fastq.gz Day3_HD_Rep2_ATAC-seq-GSM3743881.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_HD_Rep2_ATAC-seq-GSM3743881.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_HD_Rep1_ATAC-seq-GSM3743880.end1.fastq.gz Day3_HD_Rep1_ATAC-seq-GSM3743880.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_HD_Rep1_ATAC-seq-GSM3743880.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Day3_HD_Rep1_ATAC-seq-GSM3743880.end1.fastq.gz Day3_HD_Rep1_ATAC-seq-GSM3743880.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Day3_HD_Rep1_ATAC-seq-GSM3743880.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.end1.fastq.gz Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.end1.fastq.gz Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_WT_Rep2_ATAC-seq-GSM3743887.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.end1.fastq.gz Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.end1.fastq.gz Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_WT_Rep1_ATAC-seq-GSM3743886.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.end1.fastq.gz Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.end1.fastq.gz Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_HD_Rep2_ATAC-seq-GSM3743885.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.end1.fastq.gz Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.end1.fastq.gz Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Astrocyte_HD_Rep1_ATAC-seq-GSM3743884.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_WT_Rep1_ATAC-seq-GSM3743874.end1.fastq.gz PSC_WT_Rep1_ATAC-seq-GSM3743874.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_WT_Rep1_ATAC-seq-GSM3743874.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_WT_Rep1_ATAC-seq-GSM3743874.end1.fastq.gz PSC_WT_Rep1_ATAC-seq-GSM3743874.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_WT_Rep1_ATAC-seq-GSM3743874.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_HD_Rep2_ATAC-seq-GSM3743873.end1.fastq.gz PSC_HD_Rep2_ATAC-seq-GSM3743873.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_HD_Rep2_ATAC-seq-GSM3743873.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_HD_Rep2_ATAC-seq-GSM3743873.end1.fastq.gz PSC_HD_Rep2_ATAC-seq-GSM3743873.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_HD_Rep2_ATAC-seq-GSM3743873.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_HD_Rep1_ATAC-seq-GSM3743872.end1.fastq.gz PSC_HD_Rep1_ATAC-seq-GSM3743872.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_HD_Rep1_ATAC-seq-GSM3743872.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_HD_Rep1_ATAC-seq-GSM3743872.end1.fastq.gz PSC_HD_Rep1_ATAC-seq-GSM3743872.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_HD_Rep1_ATAC-seq-GSM3743872.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_WT_Rep2_ATAC-seq-GSM3743879.end1.fastq.gz NPC_WT_Rep2_ATAC-seq-GSM3743879.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_WT_Rep2_ATAC-seq-GSM3743879.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_WT_Rep2_ATAC-seq-GSM3743879.end1.fastq.gz NPC_WT_Rep2_ATAC-seq-GSM3743879.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_WT_Rep2_ATAC-seq-GSM3743879.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_WT_Rep1_ATAC-seq-GSM3743878.end1.fastq.gz NPC_WT_Rep1_ATAC-seq-GSM3743878.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_WT_Rep1_ATAC-seq-GSM3743878.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_WT_Rep1_ATAC-seq-GSM3743878.end1.fastq.gz NPC_WT_Rep1_ATAC-seq-GSM3743878.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_WT_Rep1_ATAC-seq-GSM3743878.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_HD_Rep2_ATAC-seq-GSM3743877.end1.fastq.gz NPC_HD_Rep2_ATAC-seq-GSM3743877.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_HD_Rep2_ATAC-seq-GSM3743877.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NPC_HD_Rep2_ATAC-seq-GSM3743877.end1.fastq.gz NPC_HD_Rep2_ATAC-seq-GSM3743877.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NPC_HD_Rep2_ATAC-seq-GSM3743877.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_WT_Rep2_ATAC-seq-GSM3743875.end1.fastq.gz PSC_WT_Rep2_ATAC-seq-GSM3743875.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_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_005943.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_WT_Rep2_ATAC-seq-GSM3743875.2x36mers.GCF_003339765.1_Mmul_10_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py PSC_WT_Rep2_ATAC-seq-GSM3743875.end1.fastq.gz PSC_WT_Rep2_ATAC-seq-GSM3743875.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_mulatta-Mmul_10/bowtie-indexes/chrM -p 8 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/bowtie-indexes/GCF_003339765.1_Mmul_10_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - PSC_WT_Rep2_ATAC-seq-GSM3743875.2x36mers.chrM