zcat DS20434_DNaseI-seq_up-open_flowers-GSM1289381/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20434_DNaseI-seq_up-open_flowers-GSM1289381/all.1x36mers.unique
zcat DS21513_DNaseI-seq_root_hair_cell_7_day-GSM1289376/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS21513_DNaseI-seq_root_hair_cell_7_day-GSM1289376/all.1x36mers.unique
zcat DS20427_DNaseI-seq_open_flowers-GSM1289380/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20427_DNaseI-seq_open_flowers-GSM1289380/all.1x36mers.unique
zcat DS21511_DNaseI-seq_whole_root_7_day-GSM1289374/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS21511_DNaseI-seq_whole_root_7_day-GSM1289374/all.1x36mers.unique
zcat DS21306_DNaseI-seq_seed_coat_cell_7DPA-GSM1289379/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS21306_DNaseI-seq_seed_coat_cell_7DPA-GSM1289379/all.1x36mers.unique
zcat DS20201_SE_DNaseI-seq_seed_coat_cell_4DPA-GSM1289377/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20201_SE_DNaseI-seq_seed_coat_cell_4DPA-GSM1289377/all.1x36mers.unique
zcat DS16398_DNaseI-seq_root_non_hair_cell_10_day-GSM1289375/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS16398_DNaseI-seq_root_non_hair_cell_10_day-GSM1289375/all.1x36mers.unique
zcat DS20201_PE_DNaseI-seq_seed_coat_cell_4DPA-GSM1289378/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20201_PE_DNaseI-seq_seed_coat_cell_4DPA-GSM1289378/all.1x36mers.unique