python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G11460.t1_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P247.end1.fastq.gz AL1G11460.t1_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G11460.t1_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G23550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B03-ORGi5039-96P247.end1.fastq.gz AL1G23550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G23550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G53260.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P247.end1.fastq.gz AL1G53260.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G53260.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G28980.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P247.end1.fastq.gz AL2G28980.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G28980.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G32420.t2_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P247.end1.fastq.gz AL2G32420.t2_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G32420.t2_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G40550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P247.end1.fastq.gz AL2G40550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G40550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL3G23910.t2_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P247.end1.fastq.gz AL3G23910.t2_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL3G23910.t2_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL4G38490.t1_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P247.end1.fastq.gz AL4G38490.t1_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G38490.t1_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL4G45550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P247.end1.fastq.gz AL4G45550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G45550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL8G10650.t1_S_lycopersicum_Heinz-1706-BG_DAPi712D09-ORGi5039-96P247.end1.fastq.gz AL8G10650.t1_S_lycopersicum_Heinz-1706-BG_DAPi712D09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G10650.t1_S_lycopersicum_Heinz-1706-BG_DAPi712D09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL8G13510.t2_S_lycopersicum_Heinz-1706-BG_DAPi712B08-ORGi5039-96P247.end1.fastq.gz AL8G13510.t2_S_lycopersicum_Heinz-1706-BG_DAPi712B08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G13510.t2_S_lycopersicum_Heinz-1706-BG_DAPi712B08-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G01060_S_lycopersicum_Heinz-1706-BG_DAPi712H05-ORGi5039-96P220.end1.fastq.gz AT1G01060_S_lycopersicum_Heinz-1706-BG_DAPi712H05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01060_S_lycopersicum_Heinz-1706-BG_DAPi712H05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G12260_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P220.end1.fastq.gz AT1G12260_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12260_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G13260_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P220.end1.fastq.gz AT1G13260_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G13260_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G18330_S_lycopersicum_Heinz-1706-BG_DAPi712G01-ORGi5039-96P220.end1.fastq.gz AT1G18330_S_lycopersicum_Heinz-1706-BG_DAPi712G01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G18330_S_lycopersicum_Heinz-1706-BG_DAPi712G01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20910_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P220.end1.fastq.gz AT1G20910_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20910_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20980_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P220.end1.fastq.gz AT1G20980_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20980_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G27730_S_lycopersicum_Heinz-1706-BG_DAPi712C01-ORGi5039-96P220.end1.fastq.gz AT1G27730_S_lycopersicum_Heinz-1706-BG_DAPi712C01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G27730_S_lycopersicum_Heinz-1706-BG_DAPi712C01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G29160_S_lycopersicum_Heinz-1706-BG_DAPi712B04-ORGi5039-96P220.end1.fastq.gz AT1G29160_S_lycopersicum_Heinz-1706-BG_DAPi712B04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G29160_S_lycopersicum_Heinz-1706-BG_DAPi712B04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G33240_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P220.end1.fastq.gz AT1G33240_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G33240_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G46768_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P220.end1.fastq.gz AT1G46768_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G46768_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G49480_S_lycopersicum_Heinz-1706-BG_DAPi712A04-ORGi5039-96P220.end1.fastq.gz AT1G49480_S_lycopersicum_Heinz-1706-BG_DAPi712A04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G49480_S_lycopersicum_Heinz-1706-BG_DAPi712A04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G52880_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P220.end1.fastq.gz AT1G52880_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G52880_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69180_S_lycopersicum_Heinz-1706-BG_DAPi712G05-ORGi5039-96P220.end1.fastq.gz AT1G69180_S_lycopersicum_Heinz-1706-BG_DAPi712G05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69180_S_lycopersicum_Heinz-1706-BG_DAPi712G05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69690_S_lycopersicum_Heinz-1706-BG_DAPi712C02-ORGi5039-96P220.end1.fastq.gz AT1G69690_S_lycopersicum_Heinz-1706-BG_DAPi712C02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69690_S_lycopersicum_Heinz-1706-BG_DAPi712C02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69780_S_lycopersicum_Heinz-1706-BG_DAPi712A03-ORGi5039-96P220.end1.fastq.gz AT1G69780_S_lycopersicum_Heinz-1706-BG_DAPi712A03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69780_S_lycopersicum_Heinz-1706-BG_DAPi712A03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G72740_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P220.end1.fastq.gz AT1G72740_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G72740_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G74480_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P220.end1.fastq.gz AT1G74480_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G74480_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76420_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P220.end1.fastq.gz AT1G76420_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76420_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76880_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P220.end1.fastq.gz AT1G76880_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76880_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G79580_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P220.end1.fastq.gz AT1G79580_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G79580_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G80840_S_lycopersicum_Heinz-1706-BG_DAPi712G03-ORGi5039-96P220.end1.fastq.gz AT1G80840_S_lycopersicum_Heinz-1706-BG_DAPi712G03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G80840_S_lycopersicum_Heinz-1706-BG_DAPi712G03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01060_S_lycopersicum_Heinz-1706-BG_DAPi712F05-ORGi5039-96P220.end1.fastq.gz AT2G01060_S_lycopersicum_Heinz-1706-BG_DAPi712F05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01060_S_lycopersicum_Heinz-1706-BG_DAPi712F05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01930_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P220.end1.fastq.gz AT2G01930_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01930_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01940_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P220.end1.fastq.gz AT2G01940_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01940_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G02820_S_lycopersicum_Heinz-1706-BG_DAPi712F08-ORGi5039-96P220.end1.fastq.gz AT2G02820_S_lycopersicum_Heinz-1706-BG_DAPi712F08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G02820_S_lycopersicum_Heinz-1706-BG_DAPi712F08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G18550_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P220.end1.fastq.gz AT2G18550_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G18550_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G22430_S_lycopersicum_Heinz-1706-BG_DAPi712H02-ORGi5039-96P220.end1.fastq.gz AT2G22430_S_lycopersicum_Heinz-1706-BG_DAPi712H02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G22430_S_lycopersicum_Heinz-1706-BG_DAPi712H02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G30250_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P220.end1.fastq.gz AT2G30250_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G30250_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G40620_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P220.end1.fastq.gz AT2G40620_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G40620_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45420_S_lycopersicum_Heinz-1706-BG_DAPi712F06-ORGi5039-96P220.end1.fastq.gz AT2G45420_S_lycopersicum_Heinz-1706-BG_DAPi712F06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45420_S_lycopersicum_Heinz-1706-BG_DAPi712F06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45480_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P220.end1.fastq.gz AT2G45480_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45480_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G46270_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P220.end1.fastq.gz AT2G46270_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46270_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G47070_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P220.end1.fastq.gz AT2G47070_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G47070_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G02940_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P220.end1.fastq.gz AT3G02940_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G02940_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G08500_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P220.end1.fastq.gz AT3G08500_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G08500_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G12250_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P220.end1.fastq.gz AT3G12250_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G12250_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G18990_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P220.end1.fastq.gz AT3G18990_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G18990_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G27010_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P220.end1.fastq.gz AT3G27010_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G27010_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50060_S_lycopersicum_Heinz-1706-BG_DAPi712G02-ORGi5039-96P220.end1.fastq.gz AT3G50060_S_lycopersicum_Heinz-1706-BG_DAPi712G02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50060_S_lycopersicum_Heinz-1706-BG_DAPi712G02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50260_S_lycopersicum_Heinz-1706-BG_DAPi712D02-ORGi5039-96P220.end1.fastq.gz AT3G50260_S_lycopersicum_Heinz-1706-BG_DAPi712D02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50260_S_lycopersicum_Heinz-1706-BG_DAPi712D02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50410_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P220.end1.fastq.gz AT3G50410_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50410_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G56400_S_lycopersicum_Heinz-1706-BG_DAPi712B02-ORGi5039-96P220.end1.fastq.gz AT3G56400_S_lycopersicum_Heinz-1706-BG_DAPi712B02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G56400_S_lycopersicum_Heinz-1706-BG_DAPi712B02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G57920_S_lycopersicum_Heinz-1706-BG_DAPi712D06-ORGi5039-96P220.end1.fastq.gz AT3G57920_S_lycopersicum_Heinz-1706-BG_DAPi712D06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G57920_S_lycopersicum_Heinz-1706-BG_DAPi712D06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G60530_S_lycopersicum_Heinz-1706-BG_DAPi712E05-ORGi5039-96P220.end1.fastq.gz AT3G60530_S_lycopersicum_Heinz-1706-BG_DAPi712E05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G60530_S_lycopersicum_Heinz-1706-BG_DAPi712E05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G00730_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P220.end1.fastq.gz AT4G00730_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G00730_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G14770_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P220.end1.fastq.gz AT4G14770_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G14770_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G17980_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P220.end1.fastq.gz AT4G17980_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G17980_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25470_S_lycopersicum_Heinz-1706-BG_DAPi712B06-ORGi5039-96P220.end1.fastq.gz AT4G25470_S_lycopersicum_Heinz-1706-BG_DAPi712B06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25470_S_lycopersicum_Heinz-1706-BG_DAPi712B06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25480_S_lycopersicum_Heinz-1706-BG_DAPi712F04-ORGi5039-96P220.end1.fastq.gz AT4G25480_S_lycopersicum_Heinz-1706-BG_DAPi712F04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25480_S_lycopersicum_Heinz-1706-BG_DAPi712F04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25490_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P220.end1.fastq.gz AT4G25490_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25490_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G31800_S_lycopersicum_Heinz-1706-BG_DAPi712F02-ORGi5039-96P220.end1.fastq.gz AT4G31800_S_lycopersicum_Heinz-1706-BG_DAPi712F02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G31800_S_lycopersicum_Heinz-1706-BG_DAPi712F02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G02320_S_lycopersicum_Heinz-1706-BG_DAPi712G06-ORGi5039-96P220.end1.fastq.gz AT5G02320_S_lycopersicum_Heinz-1706-BG_DAPi712G06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02320_S_lycopersicum_Heinz-1706-BG_DAPi712G06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03150_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P220.end1.fastq.gz AT5G03150_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03150_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03790_S_lycopersicum_Heinz-1706-BG_DAPi712C06-ORGi5039-96P220.end1.fastq.gz AT5G03790_S_lycopersicum_Heinz-1706-BG_DAPi712C06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03790_S_lycopersicum_Heinz-1706-BG_DAPi712C06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G05550_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P220.end1.fastq.gz AT5G05550_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G05550_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G09410_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P220.end1.fastq.gz AT5G09410_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G09410_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G10030_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P220.end1.fastq.gz AT5G10030_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G10030_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G11260_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P220.end1.fastq.gz AT5G11260_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G11260_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G14960_S_lycopersicum_Heinz-1706-BG_DAPi712E08-ORGi5039-96P220.end1.fastq.gz AT5G14960_S_lycopersicum_Heinz-1706-BG_DAPi712E08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G14960_S_lycopersicum_Heinz-1706-BG_DAPi712E08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G17300_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P220.end1.fastq.gz AT5G17300_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G17300_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G18560_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P220.end1.fastq.gz AT5G18560_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G18560_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G19790_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P220.end1.fastq.gz AT5G19790_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G19790_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G39760_S_lycopersicum_Heinz-1706-BG_DAPi712A02-ORGi5039-96P220.end1.fastq.gz AT5G39760_S_lycopersicum_Heinz-1706-BG_DAPi712A02-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G39760_S_lycopersicum_Heinz-1706-BG_DAPi712A02-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G45300_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P220.end1.fastq.gz AT5G45300_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G45300_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47390_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P220.end1.fastq.gz AT5G47390_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47390_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G52830_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P220.end1.fastq.gz AT5G52830_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52830_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G56110_S_lycopersicum_Heinz-1706-BG_DAPi712E06-ORGi5039-96P220.end1.fastq.gz AT5G56110_S_lycopersicum_Heinz-1706-BG_DAPi712E06-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G56110_S_lycopersicum_Heinz-1706-BG_DAPi712E06-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G60130_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P220.end1.fastq.gz AT5G60130_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G60130_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62020_S_lycopersicum_Heinz-1706-BG_DAPi712E04-ORGi5039-96P220.end1.fastq.gz AT5G62020_S_lycopersicum_Heinz-1706-BG_DAPi712E04-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62020_S_lycopersicum_Heinz-1706-BG_DAPi712E04-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62470_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P220.end1.fastq.gz AT5G62470_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62470_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62940_S_lycopersicum_Heinz-1706-BG_DAPi712A05-ORGi5039-96P220.end1.fastq.gz AT5G62940_S_lycopersicum_Heinz-1706-BG_DAPi712A05-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62940_S_lycopersicum_Heinz-1706-BG_DAPi712A05-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G64750_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P220.end1.fastq.gz AT5G64750_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G64750_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65410_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P220.end1.fastq.gz AT5G65410_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65410_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G67300_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P220.end1.fastq.gz AT5G67300_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G67300_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s0116.1_S_lycopersicum_Heinz-1706-BG_DAPi712C10-ORGi5039-96P247.end1.fastq.gz Carub.0001s0116.1_S_lycopersicum_Heinz-1706-BG_DAPi712C10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s0116.1_S_lycopersicum_Heinz-1706-BG_DAPi712C10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s1194.1_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P247.end1.fastq.gz Carub.0001s1194.1_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s1194.1_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s3581.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712D01-ORGi5039-96P247.end1.fastq.gz Carub.0001s3581.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712D01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s3581.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712D01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s1646.1_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P247.end1.fastq.gz Carub.0002s1646.1_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1646.1_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s1959.1_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P247.end1.fastq.gz Carub.0002s1959.1_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1959.1_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s2670.1_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P247.end1.fastq.gz Carub.0002s2670.1_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s2670.1_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0003s1161.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P247.end1.fastq.gz Carub.0003s1161.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0003s1161.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0004s2291.1_S_lycopersicum_Heinz-1706-BG_DAPi712A09-ORGi5039-96P247.end1.fastq.gz Carub.0004s2291.1_S_lycopersicum_Heinz-1706-BG_DAPi712A09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2291.1_S_lycopersicum_Heinz-1706-BG_DAPi712A09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0004s2898.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712B07-ORGi5039-96P247.end1.fastq.gz Carub.0004s2898.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712B07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2898.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712B07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0008s0039.1_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P247.end1.fastq.gz Carub.0008s0039.1_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0039.1_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0008s0285.1_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P247.end1.fastq.gz Carub.0008s0285.1_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0285.1_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P220.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P247.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P220.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P247.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P220.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P247.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P220.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P220.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P247.end1.fastq.gz Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g17260.2_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P247.end1.fastq.gz LOC_Os01g17260.2_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g17260.2_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g18240.1_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P247.end1.fastq.gz LOC_Os01g18240.1_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g18240.1_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g46970.1_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P247.end1.fastq.gz LOC_Os01g46970.1_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g46970.1_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g51154.1_S_lycopersicum_Heinz-1706-BG_DAPi712A11-ORGi5039-96P247.end1.fastq.gz LOC_Os01g51154.1_S_lycopersicum_Heinz-1706-BG_DAPi712A11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g51154.1_S_lycopersicum_Heinz-1706-BG_DAPi712A11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os02g33430.1_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P247.end1.fastq.gz LOC_Os02g33430.1_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g33430.1_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os02g42970.1_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P247.end1.fastq.gz LOC_Os02g42970.1_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g42970.1_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os03g21800.1_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P247.end1.fastq.gz LOC_Os03g21800.1_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os03g21800.1_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os06g07030.1_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P247.end1.fastq.gz LOC_Os06g07030.1_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os06g07030.1_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os08g06110.3_S_lycopersicum_Heinz-1706-BG_DAPi712D10-ORGi5039-96P247.end1.fastq.gz LOC_Os08g06110.3_S_lycopersicum_Heinz-1706-BG_DAPi712D10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g06110.3_S_lycopersicum_Heinz-1706-BG_DAPi712D10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os08g37970.1_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P247.end1.fastq.gz LOC_Os08g37970.1_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g37970.1_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os09g25060.1_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P247.end1.fastq.gz LOC_Os09g25060.1_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os09g25060.1_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os10g26500.1_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P247.end1.fastq.gz LOC_Os10g26500.1_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g26500.1_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os10g41200.1_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P247.end1.fastq.gz LOC_Os10g41200.1_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g41200.1_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc01g095460.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P247.end1.fastq.gz Solyc01g095460.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g095460.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc01g102340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P247.end1.fastq.gz Solyc01g102340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g102340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc03g116890.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P247.end1.fastq.gz Solyc03g116890.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc03g116890.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc04g078640.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P247.end1.fastq.gz Solyc04g078640.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc04g078640.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc05g007180.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P247.end1.fastq.gz Solyc05g007180.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc05g007180.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc06g048630.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P247.end1.fastq.gz Solyc06g048630.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc06g048630.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc07g040920.2.1_S_lycopersicum_Heinz-1706-BG_DAPi712B11-ORGi5039-96P247.end1.fastq.gz Solyc07g040920.2.1_S_lycopersicum_Heinz-1706-BG_DAPi712B11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc07g040920.2.1_S_lycopersicum_Heinz-1706-BG_DAPi712B11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g068320.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P247.end1.fastq.gz Solyc08g068320.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g068320.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g078340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H09-ORGi5039-96P247.end1.fastq.gz Solyc08g078340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g078340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g079120.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P247.end1.fastq.gz Solyc08g079120.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g079120.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc10g005080.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P247.end1.fastq.gz Solyc10g005080.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc10g005080.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc11g064950.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P247.end1.fastq.gz Solyc11g064950.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc11g064950.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013586407.1_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P247.end1.fastq.gz XP_013586407.1_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013586407.1_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013587350.1_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P247.end1.fastq.gz XP_013587350.1_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587350.1_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013587997.1_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P247.end1.fastq.gz XP_013587997.1_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587997.1_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013589913.1_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P247.end1.fastq.gz XP_013589913.1_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589913.1_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013589953.1_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P247.end1.fastq.gz XP_013589953.1_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589953.1_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013602769.1_S_lycopersicum_Heinz-1706-BG_DAPi712C03-ORGi5039-96P247.end1.fastq.gz XP_013602769.1_S_lycopersicum_Heinz-1706-BG_DAPi712C03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013602769.1_S_lycopersicum_Heinz-1706-BG_DAPi712C03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013609718.1_S_lycopersicum_Heinz-1706-BG_DAPi712G12-ORGi5039-96P247.end1.fastq.gz XP_013609718.1_S_lycopersicum_Heinz-1706-BG_DAPi712G12-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013609718.1_S_lycopersicum_Heinz-1706-BG_DAPi712G12-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013613838.1_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P247.end1.fastq.gz XP_013613838.1_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013613838.1_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013615900.1_S_lycopersicum_Heinz-1706-BG_DAPi712E09-ORGi5039-96P247.end1.fastq.gz XP_013615900.1_S_lycopersicum_Heinz-1706-BG_DAPi712E09-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013615900.1_S_lycopersicum_Heinz-1706-BG_DAPi712E09-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013629448.1_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P247.end1.fastq.gz XP_013629448.1_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013629448.1_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013631386.1_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P247.end1.fastq.gz XP_013631386.1_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631386.1_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013631649.1_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P247.end1.fastq.gz XP_013631649.1_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631649.1_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013634112.1_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P247.end1.fastq.gz XP_013634112.1_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P247.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19 -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/bowtie-indexes/Solanum_lycopersicum.SL2.40.19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013634112.1_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P247.PE.a