zcat Input-p1a..p1b-GSM685605_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 -  Input-p1a..p1b-GSM685605.36mers.unique
zcat Input-s1..s7-GSM685604-1_1.fastq.gz Input-s1..s7-GSM685604-2_1.fastq.gz Input-s1..s7-GSM685604-3_1.fastq.gz Input-s1..s7-GSM685604-4_1.fastq.gz Input-s1..s7-GSM685604-5_1.fastq.gz Input-s1..s7-GSM685604-6_1.fastq.gz Input-s1..s7-GSM685604-7_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 -  Input-s1..s7-GSM685604.36mers.unique
zcat SuHw-p1a..p1b-GSM685611_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 -  SuHw-p1a..p1b-GSM685611.36mers.unique
zcat SuHw-s1..s7-GSM685610-1_1.fastq.gz SuHw-s1..s7-GSM685610-2_1.fastq.gz SuHw-s1..s7-GSM685610-3_1.fastq.gz SuHw-s1..s7-GSM685610-4_1.fastq.gz SuHw-s1..s7-GSM685610-5_1.fastq.gz SuHw-s1..s7-GSM685610-6_1.fastq.gz SuHw-s1..s7-GSM685610-7_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 -  SuHw-s1..s7-GSM685610.36mers.unique