python /home/users/marinovg/code/PEFastqToTabDelimited.py ../../ENCODE4/datasets-ChIP/L30_Aiptasia_pallida_Sym_Input/L30_S2_L001_R1_001.fastq.gz ../../ENCODE4/datasets-ChIP/L30_Aiptasia_pallida_Sym_Input/L30_S2_L001_R2_001.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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L30_Aiptasia_pallida_Sym_Input.2x36mers.Aiptasia_pallida-1.0.unique
python /home/users/marinovg/code/PEFastqToTabDelimited.py ../../ENCODE4/datasets-ChIP/L32_Aiptasia_pallida_Sym_H3K27ac/L31_S3_L001_R1_001.fastq.gz ../../ENCODE4/datasets-ChIP/L32_Aiptasia_pallida_Sym_H3K27ac/L31_S3_L001_R2_001.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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L31_Aiptasia_pallida_Sym_IgG.2x36mers.Aiptasia_pallida-1.0.unique
python /home/users/marinovg/code/PEFastqToTabDelimited.py ../../ENCODE4/datasets-ChIP/L32_Aiptasia_pallida_Sym_H3K27ac/L32_S4_L001_R1_001.fastq.gz ../../ENCODE4/datasets-ChIP/L32_Aiptasia_pallida_Sym_H3K27ac/L32_S4_L001_R2_001.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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -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/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L32_Aiptasia_pallida_Sym_H3K27ac.2x36mers.Aiptasia_pallida-1.0.unique