zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep1-GSM1325785/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep1-GSM1325785/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep1-GSM1325785/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep1-GSM1325785/all.1x36mers.chrM+chloroplast.k3m2
zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep2-GSM1325786/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep2-GSM1325786/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep2-GSM1325786/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep2-GSM1325786/all.1x36mers.chrM+chloroplast.k3m2
zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep3-GSM1325787/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep3-GSM1325787/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_FLC_FRI_rep3-GSM1325787/*_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 - pSVP-SVP-GFP_svp-41_FLC_FRI_rep3-GSM1325787/all.1x36mers.chrM+chloroplast.k3m2
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep1-GSM1325788/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep1-GSM1325788/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep1-GSM1325788/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep1-GSM1325788/all.1x36mers.chrM+chloroplast.k3m2
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep2-GSM1325789/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep2-GSM1325789/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep2-GSM1325789/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep2-GSM1325789/all.1x36mers.chrM+chloroplast.k3m2
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep3-GSM1325790/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep3-GSM1325790/all.1x36mers.TAIR10.unique
zcat pSVP-SVP-GFP_svp-41_flc-3_FRI_rep3-GSM1325790/*_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 - pSVP-SVP-GFP_svp-41_flc-3_FRI_rep3-GSM1325790/all.1x36mers.chrM+chloroplast.k3m2
zcat SVP_FLC_FRI_rep1-GSM1325791/*_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 - SVP_FLC_FRI_rep1-GSM1325791/all.1x36mers.TAIR10.unique
zcat SVP_FLC_FRI_rep1-GSM1325791/*_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 - SVP_FLC_FRI_rep1-GSM1325791/all.1x36mers.chrM+chloroplast.k3m2
zcat SVP_FLC_FRI_rep2-GSM1325792/*_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 - SVP_FLC_FRI_rep2-GSM1325792/all.1x36mers.TAIR10.unique
zcat SVP_FLC_FRI_rep2-GSM1325792/*_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 - SVP_FLC_FRI_rep2-GSM1325792/all.1x36mers.chrM+chloroplast.k3m2
zcat SVP_FLC_FRI_rep3-GSM1325793/*_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 - SVP_FLC_FRI_rep3-GSM1325793/all.1x36mers.TAIR10.unique
zcat SVP_FLC_FRI_rep3-GSM1325793/*_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 - SVP_FLC_FRI_rep3-GSM1325793/all.1x36mers.chrM+chloroplast.k3m2
zcat svp-41_FLC_FRI_rep1-GSM1325794/*_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 - svp-41_FLC_FRI_rep1-GSM1325794/all.1x36mers.TAIR10.unique
zcat svp-41_FLC_FRI_rep1-GSM1325794/*_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 - svp-41_FLC_FRI_rep1-GSM1325794/all.1x36mers.chrM+chloroplast.k3m2
zcat svp-41_FLC_FRI_rep2-GSM1325795/*_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 - svp-41_FLC_FRI_rep2-GSM1325795/all.1x36mers.TAIR10.unique
zcat svp-41_FLC_FRI_rep2-GSM1325795/*_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 - svp-41_FLC_FRI_rep2-GSM1325795/all.1x36mers.chrM+chloroplast.k3m2
zcat svp-41_FLC_FRI_rep3-GSM1325796/*_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 - svp-41_FLC_FRI_rep3-GSM1325796/all.1x36mers.TAIR10.unique
zcat svp-41_FLC_FRI_rep3-GSM1325796/*_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 - svp-41_FLC_FRI_rep3-GSM1325796/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep3-GSM1325799/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep3-GSM1325799/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep3-GSM1325799/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep3-GSM1325799/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep1-GSM1325800/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep1-GSM1325800/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep1-GSM1325800/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep1-GSM1325800/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep1-GSM1325797/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep1-GSM1325797/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep1-GSM1325797/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep1-GSM1325797/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep2-GSM1325798/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep2-GSM1325798/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep2-GSM1325798/*_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 - Negative_Control_for_SVP-ChIPSeq_35S-GFP_rep2-GSM1325798/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep2-GSM1325801/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep2-GSM1325801/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep2-GSM1325801/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep2-GSM1325801/all.1x36mers.chrM+chloroplast.k3m2
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep3-GSM1325802/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep3-GSM1325802/all.1x36mers.TAIR10.unique
zcat Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep3-GSM1325802/*_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 - Negative_Control_for_FLC-ChIPSeq_svp-41_flc-3_FRI_rep3-GSM1325802/all.1x36mers.chrM+chloroplast.k3m2