zcat FUL-IM-rep1-GSM2898768/*_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 - FUL-IM-rep1-GSM2898768/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-IM-rep1-GSM2898768/*_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 - FUL-IM-rep1-GSM2898768/all.1x36mers.TAIR10.unique
zcat FUL-IM-rep2-GSM2898769/*_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 - FUL-IM-rep2-GSM2898769/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-IM-rep2-GSM2898769/*_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 - FUL-IM-rep2-GSM2898769/all.1x36mers.TAIR10.unique
zcat FUL-IM-input-GSM2898770/*_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 - FUL-IM-input-GSM2898770/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-IM-input-GSM2898770/*_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 - FUL-IM-input-GSM2898770/all.1x36mers.TAIR10.unique
zcat FUL-pistil-rep1-GSM2898771/*_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 - FUL-pistil-rep1-GSM2898771/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-pistil-rep1-GSM2898771/*_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 - FUL-pistil-rep1-GSM2898771/all.1x36mers.TAIR10.unique
zcat FUL-pistil-rep2-GSM2898772/*_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 - FUL-pistil-rep2-GSM2898772/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-pistil-rep2-GSM2898772/*_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 - FUL-pistil-rep2-GSM2898772/all.1x36mers.TAIR10.unique
zcat FUL-pistil-input-GSM2898773/*_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 - FUL-pistil-input-GSM2898773/all.1x36mers.chrM+chloroplast.k3m2
zcat FUL-pistil-input-GSM2898773/*_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 - FUL-pistil-input-GSM2898773/all.1x36mers.TAIR10.unique