python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Nipponbare-STARR-seq-library-1-GSM3428185/SRR7983752_1.fastq.gz Nipponbare-STARR-seq-library-1-GSM3428185/SRR7983752_2.fastq.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic -p 20 -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 ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Nipponbare-STARR-seq-library-1-GSM3428185/alignments.2x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Nipponbare-STARR-seq-library-2-GSM3428186/SRR7990773_1.fastq.gz Nipponbare-STARR-seq-library-2-GSM3428186/SRR7990773_2.fastq.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic -p 20 -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 ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Nipponbare-STARR-seq-library-2-GSM3428186/alignments.2x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Nipponbare-STARR-seq-input-library-1-GSM3428187/SRR7990674_1.fastq.gz Nipponbare-STARR-seq-input-library-1-GSM3428187/SRR7990674_2.fastq.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic -p 20 -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 ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Nipponbare-STARR-seq-input-library-1-GSM3428187/alignments.2x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Nipponbare-STARR-seq-input-library-2-GSM3428188/SRR7990675_1.fastq.gz Nipponbare-STARR-seq-input-library-2-GSM3428188/SRR7990675_2.fastq.gz -trim 50 50 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic -p 20 -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 ~/genomes/Land_plants/Oryza_sativa_Japonica-Nipponbare-IRGSP-1.0/bowtie-indexes/GCF_001433935.1_IRGSP-1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Nipponbare-STARR-seq-input-library-2-GSM3428188/alignments.2x50mers.unique