zcat 35S-SUC2-Input-rep1-GSM1419602/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Input-rep1-GSM1419602/all.1x36mers.TAIR10.unique
zcat 35S-SUC2-Input-rep1-GSM1419602/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Input-rep1-GSM1419602/all.1x36mers.chrM+chloroplast.k3m2
zcat 35S-SUC2-Input-rep2-GSM1419603/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Input-rep2-GSM1419603/all.1x36mers.TAIR10.unique
zcat 35S-SUC2-Input-rep2-GSM1419603/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Input-rep2-GSM1419603/all.1x36mers.chrM+chloroplast.k3m2
zcat 35S-SUC2-Myc-ChIP-rep1-GSM1419604/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Myc-ChIP-rep1-GSM1419604/all.1x36mers.TAIR10.unique
zcat 35S-SUC2-Myc-ChIP-rep1-GSM1419604/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Myc-ChIP-rep1-GSM1419604/all.1x36mers.chrM+chloroplast.k3m2
zcat 35S-SUC2-Myc-ChIP-rep2-GSM1419605/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Myc-ChIP-rep2-GSM1419605/all.1x36mers.TAIR10.unique
zcat 35S-SUC2-Myc-ChIP-rep2-GSM1419605/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - 35S-SUC2-Myc-ChIP-rep2-GSM1419605/all.1x36mers.chrM+chloroplast.k3m2
zcat MBD7-5-Input-rep1-GSM1419606/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Input-rep1-GSM1419606/all.1x36mers.TAIR10.unique
zcat MBD7-5-Input-rep1-GSM1419606/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Input-rep1-GSM1419606/all.1x36mers.chrM+chloroplast.k3m2
zcat MBD7-5-Input-rep2-GSM1419607/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Input-rep2-GSM1419607/all.1x36mers.TAIR10.unique
zcat MBD7-5-Input-rep2-GSM1419607/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Input-rep2-GSM1419607/all.1x36mers.chrM+chloroplast.k3m2
zcat MBD7-5-Myc-ChIP-rep1-GSM1419608/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Myc-ChIP-rep1-GSM1419608/all.1x36mers.TAIR10.unique
zcat MBD7-5-Myc-ChIP-rep1-GSM1419608/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Myc-ChIP-rep1-GSM1419608/all.1x36mers.chrM+chloroplast.k3m2
zcat MBD7-5-Myc-ChIP-rep2-GSM1419609/*_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/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Myc-ChIP-rep2-GSM1419609/all.1x36mers.TAIR10.unique
zcat MBD7-5-Myc-ChIP-rep2-GSM1419609/*_1.fastq.gz | python ~/code/trimfastq.py - 36 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - MBD7-5-Myc-ChIP-rep2-GSM1419609/all.1x36mers.chrM+chloroplast.k3m2