zcat prr7-3_Input_ExpI-GSM1196645/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2
zcat prr7-3_Input_ExpI-GSM1196645/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique
zcat prr7-3_IP_ExpI-GSM1196646/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2
zcat prr7-3_IP_ExpI-GSM1196646/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique
zcat prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2
zcat prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique
zcat prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2
zcat prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique
zcat prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2
zcat prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique
zcat prr7-3_IP_ExpII-GSM1196650/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique
zcat prr7-3_IP_ExpII-GSM1196650/*_1.fastq.gz | python ~/code/trimfastq.py - 35 -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 - prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2