python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_2_RNA-GSM3127705/*_1.fastq.gz Tiling_Replicate_2_RNA-GSM3127705/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_2_RNA-GSM3127705/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_1_DNA-GSM3127702/*_1.fastq.gz Tiling_Replicate_1_DNA-GSM3127702/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_1_DNA-GSM3127702/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_1_RNA-GSM3127703/*_1.fastq.gz Tiling_Replicate_1_RNA-GSM3127703/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_1_RNA-GSM3127703/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_2_DNA-GSM3127704/*_1.fastq.gz Tiling_Replicate_2_DNA-GSM3127704/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_2_DNA-GSM3127704/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_3_DNA-GSM3127706/*_1.fastq.gz Tiling_Replicate_3_DNA-GSM3127706/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_3_DNA-GSM3127706/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Tiling_Replicate_3_RNA-GSM3127707/*_1.fastq.gz Tiling_Replicate_3_RNA-GSM3127707/*_2.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/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-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Tiling_Replicate_3_RNA-GSM3127707/alignments.2x36mers.unique