python ~/code/PEFastqToTabDelimited.py Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260231/SRR4000468_1.fastq.gz Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260231/SRR4000468_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260231/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260232/SRR4000469_1.fastq.gz Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260232/SRR4000469_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260232/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260233/SRR4000470_1.fastq.gz Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260233/SRR4000470_2.fastq.gz -trim 30 30 | ~/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 - Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep1-GSM2260233/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260234/SRR4000471_1.fastq.gz Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260234/SRR4000471_2.fastq.gz -trim 30 30 | ~/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 - Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep2-GSM2260234/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_50k_root_nuclei_FANS-ATAC-seq_rep1-GSM2260235/SRR4000472_1.fastq.gz Col-0_50k_root_nuclei_FANS-ATAC-seq_rep1-GSM2260235/SRR4000472_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_root_nuclei_FANS-ATAC-seq_rep1-GSM2260235/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2-GSM2260236/SRR4000473_1.fastq.gz Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2-GSM2260236/SRR4000473_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2-GSM2260236/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep1-GSM2260237/SRR4000474_1.fastq.gz Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep1-GSM2260237/SRR4000474_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep1-GSM2260237/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep2-GSM2260238/SRR4000475_1.fastq.gz Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep2-GSM2260238/SRR4000475_2.fastq.gz -trim 30 30 | ~/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 - Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep2-GSM2260238/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py gDNA_ATAC-seq_rep1-GSM2260241/SRR4000478_1.fastq.gz gDNA_ATAC-seq_rep1-GSM2260241/SRR4000478_2.fastq.gz -trim 30 30 | ~/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 - gDNA_ATAC-seq_rep1-GSM2260241/all.2x30mers.unique
python ~/code/PEFastqToTabDelimited.py gDNA_ATAC-seq_rep2-GSM2260242/SRR4000479_1.fastq.gz gDNA_ATAC-seq_rep2-GSM2260242/SRR4000479_2.fastq.gz -trim 30 30 | ~/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 - gDNA_ATAC-seq_rep2-GSM2260242/all.2x30mers.unique