python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-APETALA2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-APETALA2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-ARF4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-ARF4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-BES1_BZR1hp2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-BES1_BZR1hp2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-BHLH1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-BHLH1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-CBF2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-CBF2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-CIP2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-CIP2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-CNR.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-CNR.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-CZFP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-CZFP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-DREB3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-DREB3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Dof4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Dof4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-EIL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-EIL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-EIL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-EIL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-EIL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-EIL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-EIL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-EIL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-ERF10.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-ERF10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-ERF9.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-ERF9.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-GRAS10.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-GRAS10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-GRAS12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-GRAS12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-GRAS4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-GRAS4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-HALO.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-HALO.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-JERF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-JERF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LAT61.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LAT61.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LES1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LES1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LOB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LOB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LOB38.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LOB38.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LOB42.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LOB42.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LSD1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LSD1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LeT12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LeT12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-LeZIP2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-LeZIP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-MADS-MC.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-MADS-MC.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-MADS-RIN.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-MADS-RIN.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-MADS1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-MADS1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-MBD5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-MBD5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-MBP7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-MBP7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-NAC-NOR.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-NAC-NOR.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-NAC6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-NAC6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-NF-YB-3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-NF-YB-3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-PTI4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-PTI4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SCL32-like.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SCL32-like.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SEPALLATA3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SEPALLATA3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_C_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_C_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_C_6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_C_6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_E_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_E_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_F_2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_F_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_F_3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_F_3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_F_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_F_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-Sl-ERF_F_5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-Sl-ERF_F_5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlBEL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlBEL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlC3H11.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlC3H11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlC3H48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlC3H48.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlCOL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlCOL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlDRP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlDRP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlDof14.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlDof14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF1a-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF1a-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF1a-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF1a-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF36.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF36.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF4-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF4-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF4-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF4-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlERF5-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlERF5-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGABL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGABL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGABL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGABL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGATA9_1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGATA9_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGATA9_2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGATA9_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGRAS3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGRAS3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlGT2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlGT2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlHB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlHB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlHZIP2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlHZIP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlHZIP3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlHZIP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMADF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMADF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYB44.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYB44.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYB70.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYB70.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYB91.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYB91.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYBL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYBL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYBL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYBL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYBL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYBL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlMYBL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlMYBL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlNAM1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlNAM1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlNAM2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlNAM2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlNAM3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlNAM3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlNAM4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlNAM4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlNAM5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlNAM5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlTCP12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlTCP12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlTCP15.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlTCP15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlTCP18.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlTCP18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWOX14.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWOX14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY11.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY23.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY23.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY40.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY40.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY41.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY41.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlWRKY81.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlWRKY81.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlYABBY2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlYABBY2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZF2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZF2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZF3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZF3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZF6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZF6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZFCL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZFCL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlZIP7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlZIP7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlbHLH014.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlbHLH014.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlbHLH138.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlbHLH138.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SlbHLH147.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SlbHLH147.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfA2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfA2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfA4a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfA4a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfA6b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfA6b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfA7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfA7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfB2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfB2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfB2b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfB2b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-SolycHsfC1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-SolycHsfC1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-TDR4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-TDR4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-TM29.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-TM29.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-VAHOX1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-VAHOX1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-cip2b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-cip2b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Green-gras6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Green-gras6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-DAP_100_C.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-DAP_100_C.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-DAP_150_D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-DAP_150_D.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-DAP_300_D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-DAP_300_D.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-DAP_50_D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-DAP_50_D.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-ampDAP_100_A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-ampDAP_100_A.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-ampDAP_150_A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-ampDAP_150_A.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-ampDAP_300_A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-ampDAP_300_A.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Green-ampDAP_50_A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Green-ampDAP_50_A.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Red-DAP_100_E.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Red-DAP_100_E.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Red-DAP_150_G.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Red-DAP_150_G.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Red-DAP_300_G.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Red-DAP_300_G.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HALO-Red-DAP_50_G.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HALO-Red-DAP_50_G.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-DAP_100_D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-DAP_100_D.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-DAP_150_E.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-DAP_150_E.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-DAP_300_E.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-DAP_300_E.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-DAP_50_E.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-DAP_50_E.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-ampDAP_100_B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-ampDAP_100_B.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-ampDAP_150_B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-ampDAP_150_B.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-ampDAP_300_B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-ampDAP_300_B.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Green-ampDAP_50_B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Green-ampDAP_50_B.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Red-DAP_100_F.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Red-DAP_100_F.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Red-DAP_150_H.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Red-DAP_150_H.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Red-DAP_300_H.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Red-DAP_300_H.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MBD5-Red-DAP_50_H.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MBD5-Red-DAP_50_H.end2.fastq.gz.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-APETALA2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-APETALA2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-ARF4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-ARF4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-BES1_BZR1hp2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-BES1_BZR1hp2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-BHLH1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-BHLH1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-CBF2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-CBF2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-CIP2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-CIP2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-CNR.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-CNR.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-CZFP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-CZFP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-DREB3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-DREB3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Dof4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Dof4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-EIL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-EIL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-EIL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-EIL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-EIL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-EIL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-EIL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-EIL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-ERF10.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-ERF10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-ERF9.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-ERF9.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-GRAS10.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-GRAS10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-GRAS12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-GRAS12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-GRAS4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-GRAS4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-HALO.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-HALO.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-JERF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-JERF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LAT61.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LAT61.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LES1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LES1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LOB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LOB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LOB38.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LOB38.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LOB42.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LOB42.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LSD1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LSD1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LeT12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LeT12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-LeZIP2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-LeZIP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-MADS-MC.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-MADS-MC.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-MADS-RIN.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-MADS-RIN.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-MADS1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-MADS1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-MBD5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-MBD5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-MBP7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-MBP7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-NAC-NOR.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-NAC-NOR.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-NAC6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-NAC6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-NF-YB-3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-NF-YB-3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-PTI4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-PTI4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SCL32-like.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SCL32-like.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SEPALLATA3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SEPALLATA3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_C_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_C_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_C_6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_C_6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_E_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_E_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_F_2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_F_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_F_3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_F_3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_F_4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_F_4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-Sl-ERF_F_5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-Sl-ERF_F_5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlBEL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlBEL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlC3H11.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlC3H11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlC3H48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlC3H48.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlCOL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlCOL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlDRP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlDRP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlDof14.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlDof14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF1a-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF1a-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF1a-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF1a-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF36.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF36.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF4-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF4-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF4-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF4-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlERF5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlERF5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGABL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGABL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGABL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGABL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGATA9_1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGATA9_1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGATA9_2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGATA9_2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGRAS3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGRAS3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlGT2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlGT2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlHB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlHB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlHZIP2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlHZIP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlHZIP3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlHZIP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMADF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMADF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYB44.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYB44.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYB70.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYB70.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYB91.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYB91.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYBL1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYBL1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYBL2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYBL2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYBL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYBL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlMYBL4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlMYBL4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlNAM1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlNAM1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlNAM2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlNAM2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlNAM3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlNAM3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlNAM4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlNAM4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlNAM5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlNAM5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlTCP12.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlTCP12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlTCP15.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlTCP15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlTCP18.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlTCP18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWOX14.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWOX14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY11.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY23.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY23.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY40.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY40.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY41.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY41.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlWRKY81.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlWRKY81.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlYABBY2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlYABBY2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZF1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZF2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZF2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZF3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZF3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZF6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZF6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZFCL3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZFCL3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZIP1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZIP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZIP3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZIP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZIP5.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZIP5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZIP6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZIP6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlZIP7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlZIP7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlbHLH014.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlbHLH014.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlbHLH138.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlbHLH138.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SlbHLH147.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SlbHLH147.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfA2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfA2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfA4a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfA4a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfA6b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfA6b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfA7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfA7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfB1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfB1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfB2a.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfB2a.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfB2b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfB2b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-SolycHsfC1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-SolycHsfC1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-TDR4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-TDR4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-TM29.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-TM29.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-VAHOX1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-VAHOX1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-cip2b.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-cip2b.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Red-gras6.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Red-gras6.1x36mers.unique