python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/Fixated_Gata1_250_a_S12_R1_001.fastq.gz /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/Fixated_Gata1_250_a_S12_R2_001.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-female -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 - 2018-10-08-Fixated_Gata1_250_a.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/NF_Gata1_250_a_S4_R1_001.fastq.gz /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/NF_Gata1_250_a_S4_R2_001.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-female -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 - 2018-10-08-NF_Gata1_250_a.2x25mers.hg19.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/NF_Gata1_250_b_S8_R1_001.fastq.gz /oak/stanford/groups/wjg/zshipony/Cut_n_Run/Plate_Fixation_Test_181008/input/NF_Gata1_250_b_S8_R2_001.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-female -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 - 2018-10-08-NF_Gata1_250_b.2x25mers.hg19.unique