zcat DP103-1-iFLMbeta-GFP-GSM1167541/*_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 - DP103-1-iFLMbeta-GFP-GSM1167541/all.1x36mers.TAIR10.unique
zcat DP103-3-iFLMbeta-GFP-GSM1167547/*_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 - DP103-3-iFLMbeta-GFP-GSM1167547/all.1x36mers.TAIR10.unique
zcat DP104-1-iFLMdelta-GFP-GSM1167543/*_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 - DP104-1-iFLMdelta-GFP-GSM1167543/all.1x36mers.TAIR10.unique
zcat DP104-4-iFLMdelta-GFP-GSM1167544/*_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 - DP104-4-iFLMdelta-GFP-GSM1167544/all.1x36mers.TAIR10.unique
zcat DP96-1-iFLMbeta-control-GSM1167540/*_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 - DP96-1-iFLMbeta-control-GSM1167540/all.1x36mers.TAIR10.unique
zcat DP96-4-iFLMbeta-control-GSM1167546/*_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 - DP96-4-iFLMbeta-control-GSM1167546/all.1x36mers.TAIR10.unique
zcat DP97-1-iFLMdelta-control-GSM1167542/*_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 - DP97-1-iFLMdelta-control-GSM1167542/all.1x36mers.TAIR10.unique
zcat DP97-4-iFLMdelta-control-GSM1167545/*_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 - DP97-4-iFLMdelta-control-GSM1167545/all.1x36mers.TAIR10.unique
zcat FLM-control-3-DP34-GSM1167553/*_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 - FLM-control-3-DP34-GSM1167553/all.1x36mers.TAIR10.unique
zcat gFLM-control-1-DP34-GSM1167550/*_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 - gFLM-control-1-DP34-GSM1167550/all.1x36mers.TAIR10.unique
zcat gFLM-control-2-DP34-GSM1167548/*_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 - gFLM-control-2-DP34-GSM1167548/all.1x36mers.TAIR10.unique
zcat gFLM-GFP-replicate-1-DP28-GSM1167551/*_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 - gFLM-GFP-replicate-1-DP28-GSM1167551/all.1x36mers.TAIR10.unique
zcat gFLM-GFP-replicate-2-DP28-GSM1167549/*_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 - gFLM-GFP-replicate-2-DP28-GSM1167549/all.1x36mers.TAIR10.unique
zcat gFLM-GFP-replicate-3-DP28-GSM1167552/*_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 - gFLM-GFP-replicate-3-DP28-GSM1167552/all.1x36mers.TAIR10.unique
zcat DP103-1-iFLMbeta-GFP-GSM1167541/*_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 - DP103-1-iFLMbeta-GFP-GSM1167541/all.1x36mers.chrM+chloroplast.k3m2
zcat DP103-3-iFLMbeta-GFP-GSM1167547/*_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 - DP103-3-iFLMbeta-GFP-GSM1167547/all.1x36mers.chrM+chloroplast.k3m2
zcat DP104-1-iFLMdelta-GFP-GSM1167543/*_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 - DP104-1-iFLMdelta-GFP-GSM1167543/all.1x36mers.chrM+chloroplast.k3m2
zcat DP104-4-iFLMdelta-GFP-GSM1167544/*_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 - DP104-4-iFLMdelta-GFP-GSM1167544/all.1x36mers.chrM+chloroplast.k3m2
zcat DP96-1-iFLMbeta-control-GSM1167540/*_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 - DP96-1-iFLMbeta-control-GSM1167540/all.1x36mers.chrM+chloroplast.k3m2
zcat DP96-4-iFLMbeta-control-GSM1167546/*_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 - DP96-4-iFLMbeta-control-GSM1167546/all.1x36mers.chrM+chloroplast.k3m2
zcat DP97-1-iFLMdelta-control-GSM1167542/*_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 - DP97-1-iFLMdelta-control-GSM1167542/all.1x36mers.chrM+chloroplast.k3m2
zcat DP97-4-iFLMdelta-control-GSM1167545/*_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 - DP97-4-iFLMdelta-control-GSM1167545/all.1x36mers.chrM+chloroplast.k3m2
zcat FLM-control-3-DP34-GSM1167553/*_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 - FLM-control-3-DP34-GSM1167553/all.1x36mers.chrM+chloroplast.k3m2
zcat gFLM-control-1-DP34-GSM1167550/*_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 - gFLM-control-1-DP34-GSM1167550/all.1x36mers.chrM+chloroplast.k3m2
zcat gFLM-control-2-DP34-GSM1167548/*_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 - gFLM-control-2-DP34-GSM1167548/all.1x36mers.chrM+chloroplast.k3m2
zcat gFLM-GFP-replicate-1-DP28-GSM1167551/*_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 - gFLM-GFP-replicate-1-DP28-GSM1167551/all.1x36mers.chrM+chloroplast.k3m2
zcat gFLM-GFP-replicate-2-DP28-GSM1167549/*_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 - gFLM-GFP-replicate-2-DP28-GSM1167549/all.1x36mers.chrM+chloroplast.k3m2
zcat gFLM-GFP-replicate-3-DP28-GSM1167552/*_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 - gFLM-GFP-replicate-3-DP28-GSM1167552/all.1x36mers.chrM+chloroplast.k3m2