python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.end1.fastq.gz ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.end1.fastq.gz ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.end1.fastq.gz ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.end1.fastq.gz ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.end1.fastq.gz ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.end1.fastq.gz ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.end1.fastq.gz ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.end1.fastq.gz ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.end1.fastq.gz ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.end1.fastq.gz ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.end1.fastq.gz ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.end1.fastq.gz ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.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/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | egrep -v NC_039630.1 | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/bowtie-indexes/Talpa_occidentalis-MPIMG_talOcc4v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique