zcat SEP3_ChIPSeq_wt_1-GSM364939/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique
zcat SEP3_ChIPSeq_wt_1-GSM364939/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2
zcat SEP3_ChIPSeq_wt_2-GSM364940/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique
zcat SEP3_ChIPSeq_wt_2-GSM364940/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2
zcat SEP3_ChIPSeq_sep3_3-GSM364941/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique
zcat SEP3_ChIPSeq_sep3_3-GSM364941/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2
zcat SEP3_ChIPSeq_wt_3-GSM364942/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique
zcat SEP3_ChIPSeq_wt_3-GSM364942/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2
zcat SEP3_ChIPSeq_ag_3-GSM364943/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique
zcat SEP3_ChIPSeq_ag_3-GSM364943/*_1.fastq.gz | python ~/code/trimfastq.py - 34 -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 - SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2