python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-APETALA2a.end1.fastq.gz Green-APETALA2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-ARF4.end1.fastq.gz Green-ARF4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-BES1_BZR1hp2.end1.fastq.gz Green-BES1_BZR1hp2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-BHLH1.end1.fastq.gz Green-BHLH1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-CBF2.end1.fastq.gz Green-CBF2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-CIP2a.end1.fastq.gz Green-CIP2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-CNR.end1.fastq.gz Green-CNR.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-CZFP1.end1.fastq.gz Green-CZFP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-DREB3.end1.fastq.gz Green-DREB3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Dof4.end1.fastq.gz Green-Dof4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-EIL1.end1.fastq.gz Green-EIL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-EIL2.end1.fastq.gz Green-EIL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-EIL3.end1.fastq.gz Green-EIL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-EIL4.end1.fastq.gz Green-EIL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-ERF10.end1.fastq.gz Green-ERF10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-ERF9.end1.fastq.gz Green-ERF9.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-GRAS10.end1.fastq.gz Green-GRAS10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-GRAS12.end1.fastq.gz Green-GRAS12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-GRAS4.end1.fastq.gz Green-GRAS4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-HALO.end1.fastq.gz Green-HALO.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-JERF1.end1.fastq.gz Green-JERF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LAT61.end1.fastq.gz Green-LAT61.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LES1.end1.fastq.gz Green-LES1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LOB1.end1.fastq.gz Green-LOB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LOB38.end1.fastq.gz Green-LOB38.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LOB42.end1.fastq.gz Green-LOB42.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LSD1.end1.fastq.gz Green-LSD1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LeT12.end1.fastq.gz Green-LeT12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-LeZIP2.end1.fastq.gz Green-LeZIP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-MADS-MC.end1.fastq.gz Green-MADS-MC.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-MADS-RIN.end1.fastq.gz Green-MADS-RIN.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-MADS1.end1.fastq.gz Green-MADS1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-MBD5.end1.fastq.gz Green-MBD5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-MBP7.end1.fastq.gz Green-MBP7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-NAC-NOR.end1.fastq.gz Green-NAC-NOR.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-NAC6.end1.fastq.gz Green-NAC6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-NF-YB-3.end1.fastq.gz Green-NF-YB-3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-PTI4.end1.fastq.gz Green-PTI4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SCL32-like.end1.fastq.gz Green-SCL32-like.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SEPALLATA3.end1.fastq.gz Green-SEPALLATA3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_C_4.end1.fastq.gz Green-Sl-ERF_C_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_C_6.end1.fastq.gz Green-Sl-ERF_C_6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_E_4.end1.fastq.gz Green-Sl-ERF_E_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_F_2.end1.fastq.gz Green-Sl-ERF_F_2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_F_3.end1.fastq.gz Green-Sl-ERF_F_3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_F_4.end1.fastq.gz Green-Sl-ERF_F_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-Sl-ERF_F_5.end1.fastq.gz Green-Sl-ERF_F_5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlBEL1.end1.fastq.gz Green-SlBEL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlC3H11.end1.fastq.gz Green-SlC3H11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlC3H48.end1.fastq.gz Green-SlC3H48.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlCOL1.end1.fastq.gz Green-SlCOL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlDRP1.end1.fastq.gz Green-SlDRP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlDof14.end1.fastq.gz Green-SlDof14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF1.end1.fastq.gz Green-SlERF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF1a-1.end1.fastq.gz Green-SlERF1a-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF1a-2.end1.fastq.gz Green-SlERF1a-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF36.end1.fastq.gz Green-SlERF36.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF4-1.end1.fastq.gz Green-SlERF4-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF4-2.end1.fastq.gz Green-SlERF4-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF5.end1.fastq.gz Green-SlERF5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlERF5-2.end1.fastq.gz Green-SlERF5-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGABL2.end1.fastq.gz Green-SlGABL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGABL4.end1.fastq.gz Green-SlGABL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGATA9_1.end1.fastq.gz Green-SlGATA9_1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGATA9_2.end1.fastq.gz Green-SlGATA9_2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGRAS3.end1.fastq.gz Green-SlGRAS3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlGT2.end1.fastq.gz Green-SlGT2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlHB1.end1.fastq.gz Green-SlHB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlHZIP2.end1.fastq.gz Green-SlHZIP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlHZIP3.end1.fastq.gz Green-SlHZIP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMADF1.end1.fastq.gz Green-SlMADF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYB44.end1.fastq.gz Green-SlMYB44.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYB70.end1.fastq.gz Green-SlMYB70.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYB91.end1.fastq.gz Green-SlMYB91.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYBL1.end1.fastq.gz Green-SlMYBL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYBL2.end1.fastq.gz Green-SlMYBL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYBL3.end1.fastq.gz Green-SlMYBL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlMYBL4.end1.fastq.gz Green-SlMYBL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlNAM1.end1.fastq.gz Green-SlNAM1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlNAM2.end1.fastq.gz Green-SlNAM2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlNAM3.end1.fastq.gz Green-SlNAM3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlNAM4.end1.fastq.gz Green-SlNAM4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlNAM5.end1.fastq.gz Green-SlNAM5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlTCP12.end1.fastq.gz Green-SlTCP12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlTCP15.end1.fastq.gz Green-SlTCP15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlTCP18.end1.fastq.gz Green-SlTCP18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWOX14.end1.fastq.gz Green-SlWOX14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY11.end1.fastq.gz Green-SlWRKY11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY23.end1.fastq.gz Green-SlWRKY23.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY40.end1.fastq.gz Green-SlWRKY40.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY41.end1.fastq.gz Green-SlWRKY41.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY6.end1.fastq.gz Green-SlWRKY6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY7.end1.fastq.gz Green-SlWRKY7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlWRKY81.end1.fastq.gz Green-SlWRKY81.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlYABBY2a.end1.fastq.gz Green-SlYABBY2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZF1.end1.fastq.gz Green-SlZF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZF2.end1.fastq.gz Green-SlZF2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZF3.end1.fastq.gz Green-SlZF3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZF6.end1.fastq.gz Green-SlZF6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZFCL3.end1.fastq.gz Green-SlZFCL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP1.end1.fastq.gz Green-SlZIP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP3.end1.fastq.gz Green-SlZIP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP4.end1.fastq.gz Green-SlZIP4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP5.end1.fastq.gz Green-SlZIP5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP6.end1.fastq.gz Green-SlZIP6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlZIP7.end1.fastq.gz Green-SlZIP7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlbHLH014.end1.fastq.gz Green-SlbHLH014.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlbHLH138.end1.fastq.gz Green-SlbHLH138.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SlbHLH147.end1.fastq.gz Green-SlbHLH147.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfA2.end1.fastq.gz Green-SolycHsfA2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfA4a.end1.fastq.gz Green-SolycHsfA4a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfA6b.end1.fastq.gz Green-SolycHsfA6b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfA7.end1.fastq.gz Green-SolycHsfA7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfB1.end1.fastq.gz Green-SolycHsfB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfB2a.end1.fastq.gz Green-SolycHsfB2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfB2b.end1.fastq.gz Green-SolycHsfB2b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-SolycHsfC1.end1.fastq.gz Green-SolycHsfC1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-TDR4.end1.fastq.gz Green-TDR4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-TM29.end1.fastq.gz Green-TM29.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-VAHOX1.end1.fastq.gz Green-VAHOX1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-cip2b.end1.fastq.gz Green-cip2b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Green-gras6.end1.fastq.gz Green-gras6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-DAP_100_C.end1.fastq.gz HALO-Green-DAP_100_C.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-DAP_150_D.end1.fastq.gz HALO-Green-DAP_150_D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-DAP_300_D.end1.fastq.gz HALO-Green-DAP_300_D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-DAP_50_D.end1.fastq.gz HALO-Green-DAP_50_D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-ampDAP_100_A.end1.fastq.gz HALO-Green-ampDAP_100_A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-ampDAP_150_A.end1.fastq.gz HALO-Green-ampDAP_150_A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-ampDAP_300_A.end1.fastq.gz HALO-Green-ampDAP_300_A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Green-ampDAP_50_A.end1.fastq.gz HALO-Green-ampDAP_50_A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Red-DAP_100_E.end1.fastq.gz HALO-Red-DAP_100_E.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Red-DAP_150_G.end1.fastq.gz HALO-Red-DAP_150_G.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Red-DAP_300_G.end1.fastq.gz HALO-Red-DAP_300_G.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HALO-Red-DAP_50_G.end1.fastq.gz HALO-Red-DAP_50_G.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-DAP_100_D.end1.fastq.gz MBD5-Green-DAP_100_D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-DAP_150_E.end1.fastq.gz MBD5-Green-DAP_150_E.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-DAP_300_E.end1.fastq.gz MBD5-Green-DAP_300_E.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-DAP_50_E.end1.fastq.gz MBD5-Green-DAP_50_E.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-ampDAP_100_B.end1.fastq.gz MBD5-Green-ampDAP_100_B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-ampDAP_150_B.end1.fastq.gz MBD5-Green-ampDAP_150_B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-ampDAP_300_B.end1.fastq.gz MBD5-Green-ampDAP_300_B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Green-ampDAP_50_B.end1.fastq.gz MBD5-Green-ampDAP_50_B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Red-DAP_100_F.end1.fastq.gz MBD5-Red-DAP_100_F.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Red-DAP_150_H.end1.fastq.gz MBD5-Red-DAP_150_H.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Red-DAP_300_H.end1.fastq.gz MBD5-Red-DAP_300_H.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MBD5-Red-DAP_50_H.end1.fastq.gz MBD5-Red-DAP_50_H.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-APETALA2a.end1.fastq.gz Red-APETALA2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-ARF4.end1.fastq.gz Red-ARF4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-BES1_BZR1hp2.end1.fastq.gz Red-BES1_BZR1hp2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-BHLH1.end1.fastq.gz Red-BHLH1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-CBF2.end1.fastq.gz Red-CBF2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-CIP2a.end1.fastq.gz Red-CIP2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-CNR.end1.fastq.gz Red-CNR.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-CZFP1.end1.fastq.gz Red-CZFP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-DREB3.end1.fastq.gz Red-DREB3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Dof4.end1.fastq.gz Red-Dof4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-EIL1.end1.fastq.gz Red-EIL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-EIL2.end1.fastq.gz Red-EIL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-EIL3.end1.fastq.gz Red-EIL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-EIL4.end1.fastq.gz Red-EIL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-ERF10.end1.fastq.gz Red-ERF10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-ERF9.end1.fastq.gz Red-ERF9.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-GRAS10.end1.fastq.gz Red-GRAS10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-GRAS12.end1.fastq.gz Red-GRAS12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-GRAS4.end1.fastq.gz Red-GRAS4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-HALO.end1.fastq.gz Red-HALO.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-JERF1.end1.fastq.gz Red-JERF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LAT61.end1.fastq.gz Red-LAT61.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LES1.end1.fastq.gz Red-LES1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LOB1.end1.fastq.gz Red-LOB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LOB38.end1.fastq.gz Red-LOB38.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LOB42.end1.fastq.gz Red-LOB42.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LSD1.end1.fastq.gz Red-LSD1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LeT12.end1.fastq.gz Red-LeT12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-LeZIP2.end1.fastq.gz Red-LeZIP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-MADS-MC.end1.fastq.gz Red-MADS-MC.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-MADS-RIN.end1.fastq.gz Red-MADS-RIN.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-MADS1.end1.fastq.gz Red-MADS1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-MBD5.end1.fastq.gz Red-MBD5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-MBP7.end1.fastq.gz Red-MBP7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-NAC-NOR.end1.fastq.gz Red-NAC-NOR.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-NAC6.end1.fastq.gz Red-NAC6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-NF-YB-3.end1.fastq.gz Red-NF-YB-3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-PTI4.end1.fastq.gz Red-PTI4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SCL32-like.end1.fastq.gz Red-SCL32-like.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SEPALLATA3.end1.fastq.gz Red-SEPALLATA3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_C_4.end1.fastq.gz Red-Sl-ERF_C_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_C_6.end1.fastq.gz Red-Sl-ERF_C_6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_E_4.end1.fastq.gz Red-Sl-ERF_E_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_F_2.end1.fastq.gz Red-Sl-ERF_F_2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_F_3.end1.fastq.gz Red-Sl-ERF_F_3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_F_4.end1.fastq.gz Red-Sl-ERF_F_4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-Sl-ERF_F_5.end1.fastq.gz Red-Sl-ERF_F_5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlBEL1.end1.fastq.gz Red-SlBEL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlC3H11.end1.fastq.gz Red-SlC3H11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlC3H48.end1.fastq.gz Red-SlC3H48.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlCOL1.end1.fastq.gz Red-SlCOL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlDRP1.end1.fastq.gz Red-SlDRP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlDof14.end1.fastq.gz Red-SlDof14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF1.end1.fastq.gz Red-SlERF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF1a-1.end1.fastq.gz Red-SlERF1a-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF1a-2.end1.fastq.gz Red-SlERF1a-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF36.end1.fastq.gz Red-SlERF36.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF4-1.end1.fastq.gz Red-SlERF4-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF4-2.end1.fastq.gz Red-SlERF4-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlERF5.end1.fastq.gz Red-SlERF5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGABL2.end1.fastq.gz Red-SlGABL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGABL4.end1.fastq.gz Red-SlGABL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGATA9_1.end1.fastq.gz Red-SlGATA9_1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGATA9_2.end1.fastq.gz Red-SlGATA9_2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGRAS3.end1.fastq.gz Red-SlGRAS3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlGT2.end1.fastq.gz Red-SlGT2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlHB1.end1.fastq.gz Red-SlHB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlHZIP2.end1.fastq.gz Red-SlHZIP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlHZIP3.end1.fastq.gz Red-SlHZIP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMADF1.end1.fastq.gz Red-SlMADF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYB44.end1.fastq.gz Red-SlMYB44.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYB70.end1.fastq.gz Red-SlMYB70.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYB91.end1.fastq.gz Red-SlMYB91.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYBL1.end1.fastq.gz Red-SlMYBL1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYBL2.end1.fastq.gz Red-SlMYBL2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYBL3.end1.fastq.gz Red-SlMYBL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlMYBL4.end1.fastq.gz Red-SlMYBL4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlNAM1.end1.fastq.gz Red-SlNAM1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlNAM2.end1.fastq.gz Red-SlNAM2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlNAM3.end1.fastq.gz Red-SlNAM3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlNAM4.end1.fastq.gz Red-SlNAM4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlNAM5.end1.fastq.gz Red-SlNAM5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlTCP12.end1.fastq.gz Red-SlTCP12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlTCP15.end1.fastq.gz Red-SlTCP15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlTCP18.end1.fastq.gz Red-SlTCP18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWOX14.end1.fastq.gz Red-SlWOX14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY11.end1.fastq.gz Red-SlWRKY11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY23.end1.fastq.gz Red-SlWRKY23.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY40.end1.fastq.gz Red-SlWRKY40.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY41.end1.fastq.gz Red-SlWRKY41.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY6.end1.fastq.gz Red-SlWRKY6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY7.end1.fastq.gz Red-SlWRKY7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlWRKY81.end1.fastq.gz Red-SlWRKY81.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlYABBY2a.end1.fastq.gz Red-SlYABBY2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZF1.end1.fastq.gz Red-SlZF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZF2.end1.fastq.gz Red-SlZF2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZF3.end1.fastq.gz Red-SlZF3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZF6.end1.fastq.gz Red-SlZF6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZFCL3.end1.fastq.gz Red-SlZFCL3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZIP1.end1.fastq.gz Red-SlZIP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZIP3.end1.fastq.gz Red-SlZIP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZIP5.end1.fastq.gz Red-SlZIP5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZIP6.end1.fastq.gz Red-SlZIP6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlZIP7.end1.fastq.gz Red-SlZIP7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlbHLH014.end1.fastq.gz Red-SlbHLH014.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlbHLH138.end1.fastq.gz Red-SlbHLH138.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SlbHLH147.end1.fastq.gz Red-SlbHLH147.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfA2.end1.fastq.gz Red-SolycHsfA2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfA4a.end1.fastq.gz Red-SolycHsfA4a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfA6b.end1.fastq.gz Red-SolycHsfA6b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfA7.end1.fastq.gz Red-SolycHsfA7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfB1.end1.fastq.gz Red-SolycHsfB1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfB2a.end1.fastq.gz Red-SolycHsfB2a.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfB2b.end1.fastq.gz Red-SolycHsfB2b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-SolycHsfC1.end1.fastq.gz Red-SolycHsfC1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-TDR4.end1.fastq.gz Red-TDR4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-TM29.end1.fastq.gz Red-TM29.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-VAHOX1.end1.fastq.gz Red-VAHOX1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-cip2b.end1.fastq.gz Red-cip2b.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Red-gras6.end1.fastq.gz Red-gras6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/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.PE.a