python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.chrM.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.chrM.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-OvaryPortion-P7-Wt-To-R2-L7298_S2-GSM3405369.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-TestisPortion-P7-Wt-To-R1-L7299_S3-GSM3405374.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.chrM.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.chrM.bam SAMstats-ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-OvaryPortion-P7-Wt-To-R1-L7297_S1-GSM3405368.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-Testis-P7-Wt-To-R1-L7279_S1-GSM3405372.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.chrM.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.chrM.bam SAMstats-ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.bam SAMstats-ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam SAMstats-ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-TestisPortion-P7-Wt-To-R2-L7300_S4-GSM3405375.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Talpa_occidentalis-MPIMG_talOcc4v2.1/Talpa_occidentalis-MPIMG_talOcc4v2.1.chrom.sizes ATAC-Testis-P7-Wt-To-R2-L7280_S2-GSM3405373.2x36mers.Talpa_occidentalis-MPIMG_talOcc4v2.1.unique.dedup.wig -notitle -RPM -uniqueBAM &