python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2-1_Diff_rep1-GSM3028917/SRR6798424_1.fastq.gz C2-1_Diff_rep1-GSM3028917/SRR6798424_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o C2-1_Diff_rep1-GSM3028917.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2-1_Undiff_rep1-GSM3028913/SRR6798420_1.fastq.gz C2-1_Undiff_rep1-GSM3028913/SRR6798420_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o C2-1_Undiff_rep1-GSM3028913.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2-2_Diff_rep1-GSM3028918/SRR6798425_1.fastq.gz C2-2_Diff_rep1-GSM3028918/SRR6798425_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o C2-2_Diff_rep1-GSM3028918.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2-2_Undiff_rep1-GSM3028914/SRR6798421_1.fastq.gz C2-2_Undiff_rep1-GSM3028914/SRR6798421_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o C2-2_Undiff_rep1-GSM3028914.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py R2-1_Diff_rep1-GSM3028919/SRR6798426_1.fastq.gz R2-1_Diff_rep1-GSM3028919/SRR6798426_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o R2-1_Diff_rep1-GSM3028919.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py R2-1_Undiff_rep1-GSM3028915/SRR6798422_1.fastq.gz R2-1_Undiff_rep1-GSM3028915/SRR6798422_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o R2-1_Undiff_rep1-GSM3028915.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py R2-2_Diff_rep1-GSM3028920/SRR6798427_1.fastq.gz R2-2_Diff_rep1-GSM3028920/SRR6798427_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o R2-2_Diff_rep1-GSM3028920.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py R2-2_Undiff_rep1-GSM3028916/SRR6798423_1.fastq.gz R2-2_Undiff_rep1-GSM3028916/SRR6798423_2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa - -o R2-2_Undiff_rep1-GSM3028916.a.e200.offrate1.bam