python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_ATCACG_R1.fastq.gz SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_ATCACG_R2.fastq.gz -trim 25 25 | /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 --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_ATCACG.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_CAGATC_R1.fastq.gz SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_CAGATC_R2.fastq.gz -trim 25 25 | /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 --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SCGPM_CUT-RUN-test1-H3K27me3_ATY4L_L1_CAGATC.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_ACTTGA_R1.fastq.gz SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_ACTTGA_R2.fastq.gz -trim 25 25 | /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 --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_ACTTGA.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_TTAGGC_R1.fastq.gz SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_TTAGGC_R2.fastq.gz -trim 25 25 | /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 --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SCGPM_CUT-RUN-test1-CTCF_AUPT0_L1_TTAGGC.2x25mers.hg19.unique