zcat D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R1.36mers.fastq; zcat D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R2.36mers.fastq; zcat D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R1.36mers.fastq; zcat D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R2.36mers.fastq; zcat D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R1.36mers.fastq; zcat D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R2.36mers.fastq; zcat D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R1.36mers.fastq; zcat D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R1.36mers.fastq,D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R1.36mers.fastq,D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R1.36mers.fastq,D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R1.36mers.fastq -2 D1-Day1-FrozKera-R3-A-AGGCAGAA-ATAGAGAG_R2.36mers.fastq,D1-Day1-FrozKera-R3-B-AGGCAGAA-GCGATCTA_R2.36mers.fastq,D1-Day1-FrozKera-R3-C-AGGCAGAA-AGAGGATA_R2.36mers.fastq,D1-Day1-FrozKera-R3-D-AGGCAGAA-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day1-FrozKera-R3-A.2x36mers.hg19-male
zcat D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R1.36mers.fastq; zcat D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R2.36mers.fastq; zcat D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R1.36mers.fastq; zcat D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R2.36mers.fastq; zcat D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R1.36mers.fastq; zcat D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R1.36mers.fastq,D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R1.36mers.fastq,D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R1.36mers.fastq -2 D1-Day3-5-FrozKera-R3-A-CAGAGAGG-ATAGAGAG_R2.36mers.fastq,D1-Day3-5-FrozKera-R3-B-CAGAGAGG-GCGATCTA_R2.36mers.fastq,D1-Day3-5-FrozKera-R3-C-CAGAGAGG-AGAGGATA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day3-5-FrozKera-R3-A.2x36mers.hg19-male
zcat D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R1.36mers.fastq; zcat D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R2.36mers.fastq; zcat D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R1.36mers.fastq; zcat D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R2.36mers.fastq; zcat D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R1.36mers.fastq; zcat D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R2.36mers.fastq; zcat D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R1.36mers.fastq; zcat D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R1.36mers.fastq,D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R1.36mers.fastq,D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R1.36mers.fastq,D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R1.36mers.fastq -2 D1-Day3-FrozKera-R3-A-CTCTCTAC-ATAGAGAG_R2.36mers.fastq,D1-Day3-FrozKera-R3-B-CTCTCTAC-GCGATCTA_R2.36mers.fastq,D1-Day3-FrozKera-R3-C-CTCTCTAC-AGAGGATA_R2.36mers.fastq,D1-Day3-FrozKera-R3-E-CTCTCTAC-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day3-FrozKera-R3-A.2x36mers.hg19-male
zcat D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R1.36mers.fastq; zcat D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R2.36mers.fastq; zcat D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R1.36mers.fastq; zcat D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R2.36mers.fastq; zcat D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R1.36mers.fastq; zcat D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R1.36mers.fastq,D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R1.36mers.fastq,D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R1.36mers.fastq -2 D1-Day4-FrozKera-R3-A-GCTACGCT-ATAGAGAG_R2.36mers.fastq,D1-Day4-FrozKera-R3-C-GCTACGCT-AGAGGATA_R2.36mers.fastq,D1-Day4-FrozKera-R3-E-GCTACGCT-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day4-FrozKera-R3-A.2x36mers.hg19-male
zcat D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R1.36mers.fastq; zcat D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R2.36mers.fastq; zcat D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R1.36mers.fastq; zcat D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R2.36mers.fastq; zcat D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R1.36mers.fastq; zcat D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R1.36mers.fastq,D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R1.36mers.fastq,D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R1.36mers.fastq -2 D1-Day5-5-FrozKera-R3-A-GTAGAGGA-ATAGAGAG_R2.36mers.fastq,D1-Day5-5-FrozKera-R3-B-GTAGAGGA-GCGATCTA_R2.36mers.fastq,D1-Day5-5-FrozKera-R3-C-GTAGAGGA-AGAGGATA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day5-5-FrozKera-R3-A.2x36mers.hg19-male
zcat D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R1.36mers.fastq; zcat D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R1.36mers.fastq -2 D1-Day5-FrozKera-R3-B-AAGAGGCA-GCGATCTA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day5-FrozKera-R3-B.2x36mers.hg19-male
zcat D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R1.36mers.fastq; zcat D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R2.36mers.fastq; zcat D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R1.36mers.fastq; zcat D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R2.36mers.fastq; zcat D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R1.36mers.fastq; zcat D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R1.36mers.fastq,D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R1.36mers.fastq,D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R1.36mers.fastq -2 D1-Day6-FrozKera-R3-A-TGGATCTG-ATAGAGAG_R2.36mers.fastq,D1-Day6-FrozKera-R3-B-TGGATCTG-GCGATCTA_R2.36mers.fastq,D1-Day6-FrozKera-R3-F-TGGATCTG-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D1-Day6-FrozKera-R3-A.2x36mers.hg19-male
zcat D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R1.36mers.fastq; zcat D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R2.36mers.fastq; zcat D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R1.36mers.fastq; zcat D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R1.36mers.fastq,D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R1.36mers.fastq -2 D2-Day4-FrozKera-R3-B-GCTACGCT-CTCCTTAC_R2.36mers.fastq,D2-Day4-FrozKera-R3-C-GCTACGCT-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-D2-Day4-FrozKera-R3-B.2x36mers.hg19-male
zcat Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R1.36mers.fastq; zcat Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R2.36mers.fastq; zcat Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R1.36mers.fastq; zcat Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R2.36mers.fastq; zcat Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R1.36mers.fastq; zcat Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R1.36mers.fastq,Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R1.36mers.fastq,Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R1.36mers.fastq -2 Day00-D2-FrozenKera-1A-TAAGGCGA-TCTACTCT_R2.36mers.fastq,Day00-D2-FrozenKera-1B-TAAGGCGA-CTCCTTAC_R2.36mers.fastq,Day00-D2-FrozenKera-1C-TAAGGCGA-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day00-D2-FrozenKera-1A.2x36mers.hg19-male
zcat Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R1.36mers.fastq; zcat Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R2.36mers.fastq; zcat Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R1.36mers.fastq; zcat Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R2.36mers.fastq; zcat Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R1.36mers.fastq; zcat Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R1.36mers.fastq,Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R1.36mers.fastq,Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R1.36mers.fastq -2 Day0-5-D1-FrozenKera-2D-CGTACTAG-GATTTCCA_R2.36mers.fastq,Day0-5-D1-FrozenKera-2E-CGTACTAG-AGGCTTAG_R2.36mers.fastq,Day0-5-D1-FrozenKera-2F-CGTACTAG-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day0-5-D1-FrozenKera-2D.2x36mers.hg19-male
zcat Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R1.36mers.fastq; zcat Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R2.36mers.fastq; zcat Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R1.36mers.fastq; zcat Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R1.36mers.fastq,Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R1.36mers.fastq -2 Day0-5-D2-FrozenKera-20-2D-CGTACTAG-ATCATGTT_R2.36mers.fastq,Day0-5-D2-FrozenKera-20-2E-CGTACTAG-TTTCATCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day0-5-D2-FrozenKera-20-2D.2x36mers.hg19-male
zcat Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R1.36mers.fastq; zcat Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R2.36mers.fastq; zcat Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R1.36mers.fastq; zcat Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R2.36mers.fastq; zcat Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R1.36mers.fastq; zcat Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R1.36mers.fastq,Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R1.36mers.fastq,Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R1.36mers.fastq -2 Day05-D2-FrozenKera-2A-CGTACTAG-TCTACTCT_R2.36mers.fastq,Day05-D2-FrozenKera-2B-CGTACTAG-CTCCTTAC_R2.36mers.fastq,Day05-D2-FrozenKera-2C-CGTACTAG-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day05-D2-FrozenKera-2A.2x36mers.hg19-male
zcat Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R1.36mers.fastq; zcat Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R2.36mers.fastq; zcat Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R1.36mers.fastq; zcat Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R1.36mers.fastq,Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R1.36mers.fastq -2 Day0-D1-FrozenKera-F-1D-TAAGGCGA-GATTTCCA_R2.36mers.fastq,Day0-D1-FrozenKera-F-1E-TAAGGCGA-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day0-D1-FrozenKera-F-1D.2x36mers.hg19-male
zcat Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R1.36mers.fastq; zcat Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R2.36mers.fastq; zcat Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R1.36mers.fastq; zcat Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R2.36mers.fastq; zcat Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R1.36mers.fastq; zcat Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R1.36mers.fastq,Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R1.36mers.fastq,Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R1.36mers.fastq -2 Day0-D2-FrozenKera-1D-TAAGGCGA-ATCATGTT_R2.36mers.fastq,Day0-D2-FrozenKera-1E-TAAGGCGA-TTTCATCA_R2.36mers.fastq,Day0-D2-FrozenKera-1F-TAAGGCGA-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day0-D2-FrozenKera-1D.2x36mers.hg19-male
zcat Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R1.36mers.fastq; zcat Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R2.36mers.fastq; zcat Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R1.36mers.fastq; zcat Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R2.36mers.fastq; zcat Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R1.36mers.fastq; zcat Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R1.36mers.fastq,Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R1.36mers.fastq,Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R1.36mers.fastq -2 Day10-D2-FrozenKera-3A-AGGCAGAA-TCTACTCT_R2.36mers.fastq,Day10-D2-FrozenKera-3B-AGGCAGAA-CTCCTTAC_R2.36mers.fastq,Day10-D2-FrozenKera-3C-AGGCAGAA-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day10-D2-FrozenKera-3A.2x36mers.hg19-male
zcat Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R1.36mers.fastq; zcat Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R2.36mers.fastq; zcat Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R1.36mers.fastq; zcat Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R2.36mers.fastq; zcat Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R1.36mers.fastq; zcat Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R1.36mers.fastq,Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R1.36mers.fastq,Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R1.36mers.fastq -2 Day1-5-D1-FrozenKera-4D-TCCTGAGC-GATTTCCA_R2.36mers.fastq,Day1-5-D1-FrozenKera-4E-TCCTGAGC-AGGCTTAG_R2.36mers.fastq,Day1-5-D1-FrozenKera-4F-TCCTGAGC-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day1-5-D1-FrozenKera-4D.2x36mers.hg19-male
zcat Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R1.36mers.fastq; zcat Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R2.36mers.fastq; zcat Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R1.36mers.fastq; zcat Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R1.36mers.fastq,Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R1.36mers.fastq -2 Day15-D2-FrozenKera-4A-TCCTGAGC-TCTACTCT_R2.36mers.fastq,Day15-D2-FrozenKera-4B-TCCTGAGC-CTCCTTAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day15-D2-FrozenKera-4A.2x36mers.hg19-male
zcat Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R1.36mers.fastq; zcat Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R2.36mers.fastq; zcat Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R1.36mers.fastq; zcat Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R1.36mers.fastq,Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R1.36mers.fastq -2 Day1-5-D2-FrozenKera-F-4D-TCCTGAGC-ATCATGTT_R2.36mers.fastq,Day1-5-D2-FrozenKera-F-4E-TCCTGAGC-TTTCATCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day1-5-D2-FrozenKera-F-4D.2x36mers.hg19-male
zcat Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R1.36mers.fastq; zcat Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R1.36mers.fastq -2 Day1-D1-FrozenKera-20-3E-AGGCAGAA-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day1-D1-FrozenKera-20-3E.2x36mers.hg19-male
zcat Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R1.36mers.fastq; zcat Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R2.36mers.fastq; zcat Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R1.36mers.fastq; zcat Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R1.36mers.fastq,Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R1.36mers.fastq -2 Day1-D2-FrozenKera-3D-AGGCAGAA-ATCATGTT_R2.36mers.fastq,Day1-D2-FrozenKera-3F-AGGCAGAA-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day1-D2-FrozenKera-3D.2x36mers.hg19-male
zcat Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R1.36mers.fastq; zcat Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R1.36mers.fastq -2 Day20-D1-FrozenKera-5C-GGACTCCT-AGAGGATA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day20-D1-FrozenKera-5C.2x36mers.hg19-male
zcat Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R1.36mers.fastq; zcat Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R2.36mers.fastq; zcat Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R1.36mers.fastq; zcat Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R2.36mers.fastq; zcat Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R1.36mers.fastq; zcat Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R1.36mers.fastq,Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R1.36mers.fastq,Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R1.36mers.fastq -2 Day20-D2-FrozenKera-5A-GGACTCCT-TCTACTCT_R2.36mers.fastq,Day20-D2-FrozenKera-5B-GGACTCCT-CTCCTTAC_R2.36mers.fastq,Day20-D2-FrozenKera-5C-GGACTCCT-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day20-D2-FrozenKera-5A.2x36mers.hg19-male
zcat Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R1.36mers.fastq; zcat Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R1.36mers.fastq -2 Day25-D1-FrozenKera-6A-TAGGCATG-ATAGAGAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day25-D1-FrozenKera-6A.2x36mers.hg19-male
zcat Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R1.36mers.fastq; zcat Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R2.36mers.fastq; zcat Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R1.36mers.fastq; zcat Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R2.36mers.fastq; zcat Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R1.36mers.fastq; zcat Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R1.36mers.fastq,Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R1.36mers.fastq,Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R1.36mers.fastq -2 Day2-5-D1-FrozenKera-6D-TAGGCATG-GATTTCCA_R2.36mers.fastq,Day2-5-D1-FrozenKera-6E-TAGGCATG-AGGCTTAG_R2.36mers.fastq,Day2-5-D1-FrozenKera-6F-TAGGCATG-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day2-5-D1-FrozenKera-6D.2x36mers.hg19-male
zcat Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R1.36mers.fastq; zcat Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R2.36mers.fastq; zcat Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R1.36mers.fastq; zcat Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R1.36mers.fastq,Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R1.36mers.fastq -2 Day25-D2-FrozenKera-6A-TAGGCATG-TCTACTCT_R2.36mers.fastq,Day25-D2-FrozenKera-6B-TAGGCATG-CTCCTTAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day25-D2-FrozenKera-6A.2x36mers.hg19-male
zcat Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R1.36mers.fastq; zcat Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R2.36mers.fastq; zcat Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R1.36mers.fastq; zcat Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R2.36mers.fastq; zcat Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R1.36mers.fastq; zcat Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R1.36mers.fastq,Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R1.36mers.fastq,Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R1.36mers.fastq -2 Day2-5-D2-FrozenKera-F-6D-TAGGCATG-ATCATGTT_R2.36mers.fastq,Day2-5-D2-FrozenKera-F-6E-TAGGCATG-TTTCATCA_R2.36mers.fastq,Day2-5-D2-FrozenKera-F-6F-TAGGCATG-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day2-5-D2-FrozenKera-F-6D.2x36mers.hg19-male
zcat Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R1.36mers.fastq; zcat Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R2.36mers.fastq; zcat Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R1.36mers.fastq; zcat Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R1.36mers.fastq,Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R1.36mers.fastq -2 Day2-D1-FrozenKera-70-5D-GGACTCCT-GATTTCCA_R2.36mers.fastq,Day2-D1-FrozenKera-70-5E-GGACTCCT-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day2-D1-FrozenKera-70-5D.2x36mers.hg19-male
zcat Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R1.36mers.fastq; zcat Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R2.36mers.fastq; zcat Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R1.36mers.fastq; zcat Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R2.36mers.fastq; zcat Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R1.36mers.fastq; zcat Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R1.36mers.fastq,Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R1.36mers.fastq,Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R1.36mers.fastq -2 Day2-D2-FrozenKera-5D-GGACTCCT-ATCATGTT_R2.36mers.fastq,Day2-D2-FrozenKera-5E-GGACTCCT-TTTCATCA_R2.36mers.fastq,Day2-D2-FrozenKera-5F-GGACTCCT-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day2-D2-FrozenKera-5D.2x36mers.hg19-male
zcat Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R1.36mers.fastq; zcat Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R2.36mers.fastq; zcat Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R1.36mers.fastq; zcat Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R2.36mers.fastq; zcat Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R1.36mers.fastq; zcat Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R1.36mers.fastq,Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R1.36mers.fastq,Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R1.36mers.fastq -2 Day30-D2-FrozenKera-7A-CTCTCTAC-TCTACTCT_R2.36mers.fastq,Day30-D2-FrozenKera-7B-CTCTCTAC-CTCCTTAC_R2.36mers.fastq,Day30-D2-FrozenKera-7C-CTCTCTAC-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day30-D2-FrozenKera-7A.2x36mers.hg19-male
zcat Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R1.36mers.fastq; zcat Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R2.36mers.fastq; zcat Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R1.36mers.fastq; zcat Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R2.36mers.fastq; zcat Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R1.36mers.fastq; zcat Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R1.36mers.fastq,Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R1.36mers.fastq,Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R1.36mers.fastq -2 Day3-5-D1-FrozenKera-8D-CAGAGAGG-GATTTCCA_R2.36mers.fastq,Day3-5-D1-FrozenKera-8E-CAGAGAGG-AGGCTTAG_R2.36mers.fastq,Day3-5-D1-FrozenKera-8F-CAGAGAGG-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day3-5-D1-FrozenKera-8D.2x36mers.hg19-male
zcat Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R1.36mers.fastq; zcat Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R2.36mers.fastq; zcat Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R1.36mers.fastq; zcat Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R1.36mers.fastq,Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R1.36mers.fastq -2 Day3-5-D2-FrozenKera-45-8D-CAGAGAGG-ATCATGTT_R2.36mers.fastq,Day3-5-D2-FrozenKera-45-8E-CAGAGAGG-TTTCATCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day3-5-D2-FrozenKera-45-8D.2x36mers.hg19-male
zcat Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R1.36mers.fastq; zcat Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R2.36mers.fastq; zcat Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R1.36mers.fastq; zcat Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R2.36mers.fastq; zcat Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R1.36mers.fastq; zcat Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R1.36mers.fastq,Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R1.36mers.fastq,Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R1.36mers.fastq -2 Day35-D2-FrozenKera-8A-CAGAGAGG-TCTACTCT_R2.36mers.fastq,Day35-D2-FrozenKera-8B-CAGAGAGG-CTCCTTAC_R2.36mers.fastq,Day35-D2-FrozenKera-8C-CAGAGAGG-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day35-D2-FrozenKera-8A.2x36mers.hg19-male
zcat Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R1.36mers.fastq; zcat Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R1.36mers.fastq -2 Day3-D1-FrozenKera-25-7D-CTCTCTAC-GATTTCCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day3-D1-FrozenKera-25-7D.2x36mers.hg19-male
zcat Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R1.36mers.fastq; zcat Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R2.36mers.fastq; zcat Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R1.36mers.fastq; zcat Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R1.36mers.fastq,Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R1.36mers.fastq -2 Day3-D2-FrozenKera-7D-CTCTCTAC-ATCATGTT_R2.36mers.fastq,Day3-D2-FrozenKera-7F-CTCTCTAC-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day3-D2-FrozenKera-7D.2x36mers.hg19-male
zcat Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R1.36mers.fastq; zcat Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R1.36mers.fastq -2 Day40-D2-FrozenKera-9A-GCTACGCT-TCTACTCT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day40-D2-FrozenKera-9A.2x36mers.hg19-male
zcat Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R1.36mers.fastq; zcat Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R1.36mers.fastq -2 Day45-D1-FrozenKera-10C-CGAGGCTG-AGAGGATA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day45-D1-FrozenKera-10C.2x36mers.hg19-male
zcat Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R1.36mers.fastq; zcat Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R2.36mers.fastq; zcat Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R1.36mers.fastq; zcat Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R2.36mers.fastq; zcat Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R1.36mers.fastq; zcat Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R1.36mers.fastq,Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R1.36mers.fastq,Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R1.36mers.fastq -2 Day4-5-D1-FrozenKera-10D-CGAGGCTG-GATTTCCA_R2.36mers.fastq,Day4-5-D1-FrozenKera-10E-CGAGGCTG-AGGCTTAG_R2.36mers.fastq,Day4-5-D1-FrozenKera-10F-CGAGGCTG-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day4-5-D1-FrozenKera-10D.2x36mers.hg19-male
zcat Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R1.36mers.fastq; zcat Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R2.36mers.fastq; zcat Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R1.36mers.fastq; zcat Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R2.36mers.fastq; zcat Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R1.36mers.fastq; zcat Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R1.36mers.fastq,Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R1.36mers.fastq,Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R1.36mers.fastq -2 Day45-D2-FrozenKera-10A-CGAGGCTG-TCTACTCT_R2.36mers.fastq,Day45-D2-FrozenKera-10B-CGAGGCTG-CTCCTTAC_R2.36mers.fastq,Day45-D2-FrozenKera-10C-CGAGGCTG-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day45-D2-FrozenKera-10A.2x36mers.hg19-male
zcat Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R1.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R2.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R1.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R2.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R1.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R2.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R1.36mers.fastq; zcat Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R1.36mers.fastq,Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R1.36mers.fastq,Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R1.36mers.fastq,Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R1.36mers.fastq -2 Day4-5-D2-FrozenKera-F-10D-CGAGGCTG-ATCATGTT_R2.36mers.fastq,Day4-5-D2-FrozenKera-F-10E-CGAGGCTG-TTTCATCA_R2.36mers.fastq,Day4-5-D2-FrozenKera-F-10F-CGAGGCTG-TACTCCTT_R2.36mers.fastq,Day4-5-D2-FrozenKera-F-10G-CCGTTTGT-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day4-5-D2-FrozenKera-F-10D.2x36mers.hg19-male
zcat Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R1.36mers.fastq; zcat Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R1.36mers.fastq -2 Day4-D1-FrozenKera-35-9D-GCTACGCT-GATTTCCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day4-D1-FrozenKera-35-9D.2x36mers.hg19-male
zcat Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R1.36mers.fastq; zcat Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R2.36mers.fastq; zcat Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R1.36mers.fastq; zcat Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R1.36mers.fastq,Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R1.36mers.fastq -2 Day4-D2-FrozenKera-9D-GCTACGCT-ATCATGTT_R2.36mers.fastq,Day4-D2-FrozenKera-9F-GCTACGCT-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day4-D2-FrozenKera-9D.2x36mers.hg19-male
zcat Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R1.36mers.fastq; zcat Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R2.36mers.fastq; zcat Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R1.36mers.fastq; zcat Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R2.36mers.fastq; zcat Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R1.36mers.fastq; zcat Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R1.36mers.fastq,Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R1.36mers.fastq,Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R1.36mers.fastq -2 Day50-D2-FrozenKera-11A-AAGAGGCA-TCTACTCT_R2.36mers.fastq,Day50-D2-FrozenKera-11B-AAGAGGCA-CTCCTTAC_R2.36mers.fastq,Day50-D2-FrozenKera-11C-AAGAGGCA-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day50-D2-FrozenKera-11A.2x36mers.hg19-male
zcat Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R1.36mers.fastq; zcat Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R1.36mers.fastq -2 Day55and60-D2_R1and3-TGGATCTG-TATGCAGT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day55and60-D2_R1and3.2x36mers.hg19-male
zcat Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R1.36mers.fastq; zcat Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R2.36mers.fastq; zcat Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R1.36mers.fastq; zcat Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R2.36mers.fastq; zcat Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R1.36mers.fastq; zcat Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R1.36mers.fastq,Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R1.36mers.fastq,Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R1.36mers.fastq -2 Day5-5-D1-FrozenKera-12D-GTAGAGGA-GATTTCCA_R2.36mers.fastq,Day5-5-D1-FrozenKera-12E-GTAGAGGA-AGGCTTAG_R2.36mers.fastq,Day5-5-D1-FrozenKera-12F-GTAGAGGA-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day5-5-D1-FrozenKera-12D.2x36mers.hg19-male
zcat Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R1.36mers.fastq; zcat Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R2.36mers.fastq; zcat Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R1.36mers.fastq; zcat Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R1.36mers.fastq,Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R1.36mers.fastq -2 Day55-D2-FrozenKera-12A-GTAGAGGA-TCTACTCT_R2.36mers.fastq,Day55-D2-FrozenKera-12B-GTAGAGGA-CTCCTTAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day55-D2-FrozenKera-12A.2x36mers.hg19-male
zcat Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R1.36mers.fastq; zcat Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R2.36mers.fastq; zcat Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R1.36mers.fastq; zcat Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R1.36mers.fastq,Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R1.36mers.fastq -2 Day5-5-D2-FrozenKera-25-12D-GTAGAGGA-ATCATGTT_R2.36mers.fastq,Day5-5-D2-FrozenKera-25-12E-GTAGAGGA-TTTCATCA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day5-5-D2-FrozenKera-25-12D.2x36mers.hg19-male
zcat Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R1.36mers.fastq; zcat Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R2.36mers.fastq; zcat Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R1.36mers.fastq; zcat Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R2.36mers.fastq; zcat Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R1.36mers.fastq; zcat Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R1.36mers.fastq,Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R1.36mers.fastq,Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R1.36mers.fastq -2 Day5-D1-FrozenKera-F-11D-AAGAGGCA-GATTTCCA_R2.36mers.fastq,Day5-D1-FrozenKera-F-11E-AAGAGGCA-AGGCTTAG_R2.36mers.fastq,Day5-D1-FrozenKera-F-11F-AAGAGGCA-AGTCCGAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day5-D1-FrozenKera-F-11D.2x36mers.hg19-male
zcat Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R1.36mers.fastq; zcat Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R2.36mers.fastq; zcat Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R1.36mers.fastq; zcat Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R2.36mers.fastq; zcat Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R1.36mers.fastq; zcat Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R1.36mers.fastq,Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R1.36mers.fastq,Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R1.36mers.fastq -2 Day5-D2-FrozenKera-11D-AAGAGGCA-ATCATGTT_R2.36mers.fastq,Day5-D2-FrozenKera-11E-AAGAGGCA-TTTCATCA_R2.36mers.fastq,Day5-D2-FrozenKera-11F-AAGAGGCA-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day5-D2-FrozenKera-11D.2x36mers.hg19-male
zcat Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R1.36mers.fastq; zcat Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R1.36mers.fastq -2 Day60-D1-FrozenKera-13C-TGGATCTG-AGAGGATA_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day60-D1-FrozenKera-13C.2x36mers.hg19-male
zcat Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R1.36mers.fastq; zcat Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R2.36mers.fastq; zcat Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R1.36mers.fastq; zcat Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R1.36mers.fastq,Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R1.36mers.fastq -2 Day60-D2-FrozenKera-13A-TGGATCTG-TCTACTCT_R2.36mers.fastq,Day60-D2-FrozenKera-13B-TGGATCTG-CTCCTTAC_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day60-D2-FrozenKera-13A.2x36mers.hg19-male
zcat Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R1.36mers.fastq; zcat Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R2.36mers.fastq; zcat Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R1.36mers.fastq; zcat Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R1.36mers.fastq,Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R1.36mers.fastq -2 Day6-D1-FrozenKera-40-13D-TGGATCTG-GATTTCCA_R2.36mers.fastq,Day6-D1-FrozenKera-40-13E-TGGATCTG-AGGCTTAG_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day6-D1-FrozenKera-40-13D.2x36mers.hg19-male
zcat Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R1.36mers.fastq; zcat Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R2.36mers.fastq; zcat Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R1.36mers.fastq; zcat Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R2.36mers.fastq; zcat Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R1.36mers.fastq; zcat Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R1.36mers.fastq,Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R1.36mers.fastq,Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R1.36mers.fastq -2 Day6-D2-FrozenKera-13D-TGGATCTG-ATCATGTT_R2.36mers.fastq,Day6-D2-FrozenKera-13E-TGGATCTG-TTTCATCA_R2.36mers.fastq,Day6-D2-FrozenKera-13F-TGGATCTG-TACTCCTT_R2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ATAC-Day6-D2-FrozenKera-13D.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.ATCACG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.CGATGT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_CTCF.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACAGTG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K27ac.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.GCCAAT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K27ac.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.ATCACG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.CGATGT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACAGTG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K4me1.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.GCCAAT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_H3K4me1.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.AGTCAA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.AGTTCC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.AGTCAA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_input_H3K4me1_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.1.36mers.fastq; zcat primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.1.36mers.fastq -2 primary_keratinocyte-d0.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.AGTTCC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d0.GGR.ChIP-seq_input_H3K4me1_CTCF.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.TTAGGC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.TGACCA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_CTCF.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.ACTTGA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K27ac.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.TAGCTT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K27ac.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.TTAGGC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.TGACCA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.ACTTGA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K4me1.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.TAGCTT.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_H3K4me1.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.ATGTCA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.CCGTCC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.ATGTCA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_input_H3K4me1_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.1.36mers.fastq; zcat primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.1.36mers.fastq -2 primary_keratinocyte-d3.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.CCGTCC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d3.GGR.ChIP-seq_input_H3K4me1_CTCF.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b1.t1.CAGATC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_CTCF.b2.t1.GATCAG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_CTCF.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b1.t1.GGCTAC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K27ac.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27ac.b2.t1.CTTGTA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K27ac.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b1.t1.CAGATC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K27me3.b2.t1.GATCAG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b1.t1.GGCTAC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K4me1.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_H3K4me1.b2.t1.CTTGTA.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_H3K4me1.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b1.t1.GTAGAG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K27ac_H3K27me3.b2.t1.GTCCGC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_input_H3K27ac_H3K27me3.b2.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b1.t1.GTAGAG.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_input_H3K4me1_CTCF.b1.2x36mers.hg19-male
zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.1.36mers.fastq; zcat primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout >  primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.2.36mers.fastq;  /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam -1 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.1.36mers.fastq -2 primary_keratinocyte-d6.GGR.Stanford_Snyder.ChIP-seq_input_H3K4me1_CTCF.b2.t1.GTCCGC.2.36mers.fastq | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - primary_keratinocyte-d6.GGR.ChIP-seq_input_H3K4me1_CTCF.b2.2x36mers.hg19-male