zcat DS19992_SE_DNaseI-seq_7_day_old_seedling_Control-GSM1289362/SRR1049781_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 - DS19992_SE_DNaseI-seq_7_day_old_seedling_Control-GSM1289362/all.1x36mers.unique
zcat DS20412_SE_DNaseI-seq_7_day_old_seedling_Dark_3hr_light-GSM1289354/SRR1049773_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 - DS20412_SE_DNaseI-seq_7_day_old_seedling_Dark_3hr_light-GSM1289354/all.1x36mers.unique
zcat DS20423_SE_DNaseI-seq_7_day_old_seedling_Heat_Shock-GSM1289360/SRR1049779_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 - DS20423_SE_DNaseI-seq_7_day_old_seedling_Heat_Shock-GSM1289360/all.1x36mers.unique
zcat DS20968_SE_DNaseI-seq_7_day_old_seedling_Dark_24hr-GSM1289350/SRR1049769_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 - DS20968_SE_DNaseI-seq_7_day_old_seedling_Dark_24hr-GSM1289350/all.1x36mers.unique
zcat DS21094_SE_DNaseI-seq_7_day_old_seedling_Control-GSM1289358/SRR1049777_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 - DS21094_SE_DNaseI-seq_7_day_old_seedling_Control-GSM1289358/all.1x36mers.unique
zcat DS22138_SE_DNaseI-seq_7_day_old_seedling_Dark-GSM1289356/SRR1049775_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 - DS22138_SE_DNaseI-seq_7_day_old_seedling_Dark-GSM1289356/all.1x36mers.unique
zcat DS22140_SE_DNaseI-seq_7_day_old_seedling_Dark_30min_light-GSM1289352/SRR1049771_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 - DS22140_SE_DNaseI-seq_7_day_old_seedling_Dark_30min_light-GSM1289352/all.1x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS19992_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289363/SRR1049782_1.fastq.gz DS19992_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289363/SRR1049782_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS19992_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289363/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS20412_PE_DNaseI-seq_7_day_old_seedling_Dark_3hr_light-GSM1289355/SRR1049774_1.fastq.gz DS20412_PE_DNaseI-seq_7_day_old_seedling_Dark_3hr_light-GSM1289355/SRR1049774_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20412_PE_DNaseI-seq_7_day_old_seedling_Dark_3hr_light-GSM1289355/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS20423_PE_DNaseI-seq_7_day_old_seedling_Heat_Shock-GSM1289361/SRR1049780_1.fastq.gz DS20423_PE_DNaseI-seq_7_day_old_seedling_Heat_Shock-GSM1289361/SRR1049780_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20423_PE_DNaseI-seq_7_day_old_seedling_Heat_Shock-GSM1289361/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS20968_PE_DNaseI-seq_7_day_old_seedling_Dark_24hr-GSM1289351/SRR1049770_1.fastq.gz DS20968_PE_DNaseI-seq_7_day_old_seedling_Dark_24hr-GSM1289351/SRR1049770_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS20968_PE_DNaseI-seq_7_day_old_seedling_Dark_24hr-GSM1289351/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS21094_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289359/SRR1049778_1.fastq.gz DS21094_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289359/SRR1049778_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS21094_PE_DNaseI-seq_7_day_old_seedling_Control-GSM1289359/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS22138_PE_DNaseI-seq_7_day_old_seedling_Dark-GSM1289357/SRR1049776_1.fastq.gz DS22138_PE_DNaseI-seq_7_day_old_seedling_Dark-GSM1289357/SRR1049776_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS22138_PE_DNaseI-seq_7_day_old_seedling_Dark-GSM1289357/all.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py DS22140_PE_DNaseI-seq_7_day_old_seedling_Dark_30min_light-GSM1289353/SRR1049772_1.fastq.gz DS22140_PE_DNaseI-seq_7_day_old_seedling_Dark_30min_light-GSM1289353/SRR1049772_2.fastq.gz -trim 36 36 | ~/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 -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - DS22140_PE_DNaseI-seq_7_day_old_seedling_Dark_30min_light-GSM1289353/all.2x36mers.unique