python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL190_SHAREseq_A549_p53_ATAC_1_3.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz BL190_SHAREseq_A549_p53_ATAC_1_3.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL191_SHAREseq_A549_p53_ATAC_1_4.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL191_SHAREseq_A549_p53_ATAC_1_4/BL191_SHAREseq_A549_p53_ATAC_1_4.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end1.fastq.gz BL191_SHAREseq_A549_p53_ATAC_1_4.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL191_SHAREseq_A549_p53_ATAC_1_4/BL191_SHAREseq_A549_p53_ATAC_1_4.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL192_SHAREseq_A549_p53_ATAC_2_1.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz BL192_SHAREseq_A549_p53_ATAC_2_1.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL193_SHAREseq_A549_p53_ATAC_2_2.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL193_SHAREseq_A549_p53_ATAC_2_2/BL193_SHAREseq_A549_p53_ATAC_2_2.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end1.fastq.gz BL193_SHAREseq_A549_p53_ATAC_2_2.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL193_SHAREseq_A549_p53_ATAC_2_2/BL193_SHAREseq_A549_p53_ATAC_2_2.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM -p 20 -v 2 -a -t --best --strata -q -X 1000 --sam-nh --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL190_SHAREseq_A549_p53_ATAC_1_3.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz BL190_SHAREseq_A549_p53_ATAC_1_3.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL190_SHAREseq_A549_p53_ATAC_1_3.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL191_SHAREseq_A549_p53_ATAC_1_4.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL191_SHAREseq_A549_p53_ATAC_1_4/BL191_SHAREseq_A549_p53_ATAC_1_4.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end1.fastq.gz BL191_SHAREseq_A549_p53_ATAC_1_4.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL191_SHAREseq_A549_p53_ATAC_1_4/BL191_SHAREseq_A549_p53_ATAC_1_4.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL191_SHAREseq_A549_p53_ATAC_1_4.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL192_SHAREseq_A549_p53_ATAC_2_1.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz BL192_SHAREseq_A549_p53_ATAC_2_1.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL192_SHAREseq_A549_p53_ATAC_2_1.2x36mers.hg38.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py BL193_SHAREseq_A549_p53_ATAC_2_2.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end1.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL193_SHAREseq_A549_p53_ATAC_2_2/BL193_SHAREseq_A549_p53_ATAC_2_2.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end1.fastq.gz BL193_SHAREseq_A549_p53_ATAC_2_2.221021_A00509_0631_BH73N3DSX5.barcodes_annotated.end2.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-SHARE-seq/BL193_SHAREseq_A549_p53_ATAC_2_2/BL193_SHAREseq_A549_p53_ATAC_2_2.220913_NB551514_0815_AH2YTWBGXM.barcodes_annotated.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam-nh --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BL193_SHAREseq_A549_p53_ATAC_2_2.2x36mers.hg38.unique