zcat ChIP_MSL2_S2_rep4-GSM2469514_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_MSL2_S2_rep4-GSM2469514.36mers.unique
zcat ChIP_MSL2_S2_rep3-GSM2469512_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_MSL2_S2_rep3-GSM2469512.36mers.unique
zcat ChIP_MSL2_S2_rep2-GSM2469510_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_MSL2_S2_rep2-GSM2469510.36mers.unique
zcat ChIP_MSL2_S2_rep1-GSM2469507_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_MSL2_S2_rep1-GSM2469507.36mers.unique
zcat ChIP_Input_S2_rep4-GSM2469513_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_Input_S2_rep4-GSM2469513.36mers.unique
zcat ChIP_Input_S2_rep3-GSM2469511_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_Input_S2_rep3-GSM2469511.36mers.unique
zcat ChIP_Input_S2_rep2-GSM246950_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_Input_S2_rep2-GSM246950.36mers.unique
zcat ChIP_Input_S2_rep1-GSM2469506_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_Input_S2_rep1-GSM2469506.36mers.unique
zcat ChIP_H4K16ac_S2_rep1-GSM2469508_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort -  ChIP_H4K16ac_S2_rep1-GSM2469508.36mers.unique