python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G11460.t1_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P247.end1.fastq.gz AL1G11460.t1_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G11460.t1_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G23550.t1_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P247.end1.fastq.gz AL1G23550.t1_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G23550.t1_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL1G53260.t1_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P247.end1.fastq.gz AL1G53260.t1_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G53260.t1_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G28980.t1_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P247.end1.fastq.gz AL2G28980.t1_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G28980.t1_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G32420.t2_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P247.end1.fastq.gz AL2G32420.t2_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G32420.t2_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL2G40550.t1_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P247.end1.fastq.gz AL2G40550.t1_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G40550.t1_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL3G23910.t2_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P247.end1.fastq.gz AL3G23910.t2_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL3G23910.t2_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL4G38490.t1_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P247.end1.fastq.gz AL4G38490.t1_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G38490.t1_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL4G45550.t1_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P247.end1.fastq.gz AL4G45550.t1_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G45550.t1_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL8G10650.t1_B_oleracea_TO1000DH3_DAPi712D09-ORGi5021-96P247.end1.fastq.gz AL8G10650.t1_B_oleracea_TO1000DH3_DAPi712D09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G10650.t1_B_oleracea_TO1000DH3_DAPi712D09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AL8G13510.t2_B_oleracea_TO1000DH3_DAPi712B08-ORGi5021-96P247.end1.fastq.gz AL8G13510.t2_B_oleracea_TO1000DH3_DAPi712B08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G13510.t2_B_oleracea_TO1000DH3_DAPi712B08-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G01060_B_oleracea_TO1000DH3_DAPi709D10-ORGi5021-96P169.end1.fastq.gz AT1G01060_B_oleracea_TO1000DH3_DAPi709D10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01060_B_oleracea_TO1000DH3_DAPi709D10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G01060_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P220.end1.fastq.gz AT1G01060_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01060_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G01250_B_oleracea_TO1000DH3_DAPi710B07-ORGi5021-96P151.end1.fastq.gz AT1G01250_B_oleracea_TO1000DH3_DAPi710B07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01250_B_oleracea_TO1000DH3_DAPi710B07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G01720_B_oleracea_TO1000DH3_DAPi709F09-ORGi5021-96P169.end1.fastq.gz AT1G01720_B_oleracea_TO1000DH3_DAPi709F09-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01720_B_oleracea_TO1000DH3_DAPi709F09-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G02230_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P155.end1.fastq.gz AT1G02230_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G02230_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G02250_B_oleracea_TO1000DH3_DAPi710D09-ORGi5021-96P151.end1.fastq.gz AT1G02250_B_oleracea_TO1000DH3_DAPi710D09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G02250_B_oleracea_TO1000DH3_DAPi710D09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G03800_B_oleracea_TO1000DH3_DAPi709C01-ORGi5021-96P169.end1.fastq.gz AT1G03800_B_oleracea_TO1000DH3_DAPi709C01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G03800_B_oleracea_TO1000DH3_DAPi709C01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G06280_B_oleracea_TO1000DH3_DAPi710H02-ORGi5021-96P151.end1.fastq.gz AT1G06280_B_oleracea_TO1000DH3_DAPi710H02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G06280_B_oleracea_TO1000DH3_DAPi710H02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G06850_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P155.end1.fastq.gz AT1G06850_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G06850_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G08320_B_oleracea_TO1000DH3_DAPi710D12-ORGi5021-96P151.end1.fastq.gz AT1G08320_B_oleracea_TO1000DH3_DAPi710D12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G08320_B_oleracea_TO1000DH3_DAPi710D12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G09540_B_oleracea_TO1000DH3_DAPi710F07-ORGi5021-96P151.end1.fastq.gz AT1G09540_B_oleracea_TO1000DH3_DAPi710F07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G09540_B_oleracea_TO1000DH3_DAPi710F07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G12260_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P155.end1.fastq.gz AT1G12260_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12260_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G12260_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P220.end1.fastq.gz AT1G12260_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12260_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G12610_B_oleracea_TO1000DH3_DAPi710A11-ORGi5021-96P151.end1.fastq.gz AT1G12610_B_oleracea_TO1000DH3_DAPi710A11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12610_B_oleracea_TO1000DH3_DAPi710A11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G12630_B_oleracea_TO1000DH3_DAPi710B04-ORGi5021-96P151.end1.fastq.gz AT1G12630_B_oleracea_TO1000DH3_DAPi710B04-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12630_B_oleracea_TO1000DH3_DAPi710B04-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G13260_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P220.end1.fastq.gz AT1G13260_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G13260_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G13600_B_oleracea_TO1000DH3_DAPi712F12-ORGi5021-96P155.end1.fastq.gz AT1G13600_B_oleracea_TO1000DH3_DAPi712F12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G13600_B_oleracea_TO1000DH3_DAPi712F12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G14687_B_oleracea_TO1000DH3_DAPi711F04-ORGi5021-96P166.end1.fastq.gz AT1G14687_B_oleracea_TO1000DH3_DAPi711F04-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G14687_B_oleracea_TO1000DH3_DAPi711F04-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G16490_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P155.end1.fastq.gz AT1G16490_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G16490_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G18330_B_oleracea_TO1000DH3_DAPi711F03-ORGi5021-96P166.end1.fastq.gz AT1G18330_B_oleracea_TO1000DH3_DAPi711F03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G18330_B_oleracea_TO1000DH3_DAPi711F03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G18330_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P220.end1.fastq.gz AT1G18330_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G18330_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G19000_B_oleracea_TO1000DH3_DAPi711D11-ORGi5021-96P166.end1.fastq.gz AT1G19000_B_oleracea_TO1000DH3_DAPi711D11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G19000_B_oleracea_TO1000DH3_DAPi711D11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G19210_B_oleracea_TO1000DH3_DAPi709H02-ORGi5021-96P169.end1.fastq.gz AT1G19210_B_oleracea_TO1000DH3_DAPi709H02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G19210_B_oleracea_TO1000DH3_DAPi709H02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20910_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P220.end1.fastq.gz AT1G20910_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20910_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20910_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P155.end1.fastq.gz AT1G20910_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20910_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20980_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P155.end1.fastq.gz AT1G20980_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20980_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G20980_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P220.end1.fastq.gz AT1G20980_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20980_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G22070_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P155.end1.fastq.gz AT1G22070_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G22070_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G22810_B_oleracea_TO1000DH3_DAPi709B04-ORGi5021-96P169.end1.fastq.gz AT1G22810_B_oleracea_TO1000DH3_DAPi709B04-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G22810_B_oleracea_TO1000DH3_DAPi709B04-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G25340_B_oleracea_TO1000DH3_DAPi710B01-ORGi5021-96P151.end1.fastq.gz AT1G25340_B_oleracea_TO1000DH3_DAPi710B01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G25340_B_oleracea_TO1000DH3_DAPi710B01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G25550_B_oleracea_TO1000DH3_DAPi711C01-ORGi5021-96P166.end1.fastq.gz AT1G25550_B_oleracea_TO1000DH3_DAPi711C01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G25550_B_oleracea_TO1000DH3_DAPi711C01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G27730_B_oleracea_TO1000DH3_DAPi711F01-ORGi5021-96P166.end1.fastq.gz AT1G27730_B_oleracea_TO1000DH3_DAPi711F01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G27730_B_oleracea_TO1000DH3_DAPi711F01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G27730_B_oleracea_TO1000DH3_DAPi712C01-ORGi5021-96P220.end1.fastq.gz AT1G27730_B_oleracea_TO1000DH3_DAPi712C01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G27730_B_oleracea_TO1000DH3_DAPi712C01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G28160_B_oleracea_TO1000DH3_DAPi710E04-ORGi5021-96P151.end1.fastq.gz AT1G28160_B_oleracea_TO1000DH3_DAPi710E04-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G28160_B_oleracea_TO1000DH3_DAPi710E04-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G28370_B_oleracea_TO1000DH3_DAPi709A07-ORGi5021-96P169.end1.fastq.gz AT1G28370_B_oleracea_TO1000DH3_DAPi709A07-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G28370_B_oleracea_TO1000DH3_DAPi709A07-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G28470_B_oleracea_TO1000DH3_DAPi710E12-ORGi5021-96P151.end1.fastq.gz AT1G28470_B_oleracea_TO1000DH3_DAPi710E12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G28470_B_oleracea_TO1000DH3_DAPi710E12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G29160_B_oleracea_TO1000DH3_DAPi709G01-ORGi5021-96P169.end1.fastq.gz AT1G29160_B_oleracea_TO1000DH3_DAPi709G01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G29160_B_oleracea_TO1000DH3_DAPi709G01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G29160_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P220.end1.fastq.gz AT1G29160_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G29160_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G29280_B_oleracea_TO1000DH3_DAPi711F12-ORGi5021-96P166.end1.fastq.gz AT1G29280_B_oleracea_TO1000DH3_DAPi711F12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G29280_B_oleracea_TO1000DH3_DAPi711F12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G30210_B_oleracea_TO1000DH3_DAPi711E03-ORGi5021-96P166.end1.fastq.gz AT1G30210_B_oleracea_TO1000DH3_DAPi711E03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G30210_B_oleracea_TO1000DH3_DAPi711E03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G32150_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P155.end1.fastq.gz AT1G32150_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G32150_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G33240_B_oleracea_TO1000DH3_DAPi711C10-ORGi5021-96P166.end1.fastq.gz AT1G33240_B_oleracea_TO1000DH3_DAPi711C10-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G33240_B_oleracea_TO1000DH3_DAPi711C10-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G33240_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P220.end1.fastq.gz AT1G33240_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G33240_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G34670_B_oleracea_TO1000DH3_DAPi710G09-ORGi5021-96P151.end1.fastq.gz AT1G34670_B_oleracea_TO1000DH3_DAPi710G09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G34670_B_oleracea_TO1000DH3_DAPi710G09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G36060_B_oleracea_TO1000DH3_DAPi709D02-ORGi5021-96P169.end1.fastq.gz AT1G36060_B_oleracea_TO1000DH3_DAPi709D02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G36060_B_oleracea_TO1000DH3_DAPi709D02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G43700_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P155.end1.fastq.gz AT1G43700_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G43700_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G46768_B_oleracea_TO1000DH3_DAPi709H03-ORGi5021-96P169.end1.fastq.gz AT1G46768_B_oleracea_TO1000DH3_DAPi709H03-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G46768_B_oleracea_TO1000DH3_DAPi709H03-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G46768_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P220.end1.fastq.gz AT1G46768_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G46768_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G47655_B_oleracea_TO1000DH3_DAPi710D05-ORGi5021-96P151.end1.fastq.gz AT1G47655_B_oleracea_TO1000DH3_DAPi710D05-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G47655_B_oleracea_TO1000DH3_DAPi710D05-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G49010_B_oleracea_TO1000DH3_DAPi709F03-ORGi5021-96P169.end1.fastq.gz AT1G49010_B_oleracea_TO1000DH3_DAPi709F03-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G49010_B_oleracea_TO1000DH3_DAPi709F03-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G49480_B_oleracea_TO1000DH3_DAPi711D12-ORGi5021-96P166.end1.fastq.gz AT1G49480_B_oleracea_TO1000DH3_DAPi711D12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G49480_B_oleracea_TO1000DH3_DAPi711D12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G49480_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P220.end1.fastq.gz AT1G49480_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G49480_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G50640_B_oleracea_TO1000DH3_DAPi709G04-ORGi5021-96P169.end1.fastq.gz AT1G50640_B_oleracea_TO1000DH3_DAPi709G04-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G50640_B_oleracea_TO1000DH3_DAPi709G04-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G51220_B_oleracea_TO1000DH3_DAPi709G12-ORGi5021-96P169.end1.fastq.gz AT1G51220_B_oleracea_TO1000DH3_DAPi709G12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G51220_B_oleracea_TO1000DH3_DAPi709G12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G52880_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P155.end1.fastq.gz AT1G52880_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G52880_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G52880_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P220.end1.fastq.gz AT1G52880_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G52880_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G53170_B_oleracea_TO1000DH3_DAPi711H11-ORGi5021-96P166.end1.fastq.gz AT1G53170_B_oleracea_TO1000DH3_DAPi711H11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G53170_B_oleracea_TO1000DH3_DAPi711H11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G53230_B_oleracea_TO1000DH3_DAPi709C08-ORGi5021-96P169.end1.fastq.gz AT1G53230_B_oleracea_TO1000DH3_DAPi709C08-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G53230_B_oleracea_TO1000DH3_DAPi709C08-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G63030_B_oleracea_TO1000DH3_DAPi710C07-ORGi5021-96P151.end1.fastq.gz AT1G63030_B_oleracea_TO1000DH3_DAPi710C07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G63030_B_oleracea_TO1000DH3_DAPi710C07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G64620_B_oleracea_TO1000DH3_DAPi711C04-ORGi5021-96P166.end1.fastq.gz AT1G64620_B_oleracea_TO1000DH3_DAPi711C04-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G64620_B_oleracea_TO1000DH3_DAPi711C04-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G68320_B_oleracea_TO1000DH3_DAPi709H11-ORGi5021-96P169.end1.fastq.gz AT1G68320_B_oleracea_TO1000DH3_DAPi709H11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G68320_B_oleracea_TO1000DH3_DAPi709H11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69180_B_oleracea_TO1000DH3_DAPi709G09-ORGi5021-96P169.end1.fastq.gz AT1G69180_B_oleracea_TO1000DH3_DAPi709G09-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69180_B_oleracea_TO1000DH3_DAPi709G09-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69180_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P220.end1.fastq.gz AT1G69180_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69180_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69490_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P155.end1.fastq.gz AT1G69490_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69490_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69570_B_oleracea_TO1000DH3_DAPi710F11-ORGi5021-96P151.end1.fastq.gz AT1G69570_B_oleracea_TO1000DH3_DAPi710F11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69570_B_oleracea_TO1000DH3_DAPi710F11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69690_B_oleracea_TO1000DH3_DAPi711G05-ORGi5021-96P166.end1.fastq.gz AT1G69690_B_oleracea_TO1000DH3_DAPi711G05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69690_B_oleracea_TO1000DH3_DAPi711G05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69690_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P220.end1.fastq.gz AT1G69690_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69690_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69780_B_oleracea_TO1000DH3_DAPi711G07-ORGi5021-96P166.end1.fastq.gz AT1G69780_B_oleracea_TO1000DH3_DAPi711G07-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69780_B_oleracea_TO1000DH3_DAPi711G07-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G69780_B_oleracea_TO1000DH3_DAPi712A03-ORGi5021-96P220.end1.fastq.gz AT1G69780_B_oleracea_TO1000DH3_DAPi712A03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69780_B_oleracea_TO1000DH3_DAPi712A03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G71450_B_oleracea_TO1000DH3_DAPi709G11-ORGi5021-96P169.end1.fastq.gz AT1G71450_B_oleracea_TO1000DH3_DAPi709G11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G71450_B_oleracea_TO1000DH3_DAPi709G11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G72010_B_oleracea_TO1000DH3_DAPi711H03-ORGi5021-96P166.end1.fastq.gz AT1G72010_B_oleracea_TO1000DH3_DAPi711H03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G72010_B_oleracea_TO1000DH3_DAPi711H03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G72740_B_oleracea_TO1000DH3_DAPi710H11-ORGi5021-96P151.end1.fastq.gz AT1G72740_B_oleracea_TO1000DH3_DAPi710H11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G72740_B_oleracea_TO1000DH3_DAPi710H11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G72740_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P220.end1.fastq.gz AT1G72740_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G72740_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G74480_B_oleracea_TO1000DH3_DAPi710H04-ORGi5021-96P151.end1.fastq.gz AT1G74480_B_oleracea_TO1000DH3_DAPi710H04-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G74480_B_oleracea_TO1000DH3_DAPi710H04-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G74480_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P220.end1.fastq.gz AT1G74480_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G74480_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G74650_B_oleracea_TO1000DH3_DAPi710H08-ORGi5021-96P151.end1.fastq.gz AT1G74650_B_oleracea_TO1000DH3_DAPi710H08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G74650_B_oleracea_TO1000DH3_DAPi710H08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G75240_B_oleracea_TO1000DH3_DAPi710C12-ORGi5021-96P151.end1.fastq.gz AT1G75240_B_oleracea_TO1000DH3_DAPi710C12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G75240_B_oleracea_TO1000DH3_DAPi710C12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G75390_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P155.end1.fastq.gz AT1G75390_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G75390_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76420_B_oleracea_TO1000DH3_DAPi710C10-ORGi5021-96P151.end1.fastq.gz AT1G76420_B_oleracea_TO1000DH3_DAPi710C10-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76420_B_oleracea_TO1000DH3_DAPi710C10-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76420_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P220.end1.fastq.gz AT1G76420_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76420_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76880_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P155.end1.fastq.gz AT1G76880_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76880_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G76880_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P220.end1.fastq.gz AT1G76880_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76880_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G77200_B_oleracea_TO1000DH3_DAPi710C05-ORGi5021-96P151.end1.fastq.gz AT1G77200_B_oleracea_TO1000DH3_DAPi710C05-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G77200_B_oleracea_TO1000DH3_DAPi710C05-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G79180_B_oleracea_TO1000DH3_DAPi709H09-ORGi5021-96P169.end1.fastq.gz AT1G79180_B_oleracea_TO1000DH3_DAPi709H09-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G79180_B_oleracea_TO1000DH3_DAPi709H09-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G79580_B_oleracea_TO1000DH3_DAPi710H09-ORGi5021-96P151.end1.fastq.gz AT1G79580_B_oleracea_TO1000DH3_DAPi710H09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G79580_B_oleracea_TO1000DH3_DAPi710H09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G79580_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P220.end1.fastq.gz AT1G79580_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G79580_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G80840_B_oleracea_TO1000DH3_DAPi711A11-ORGi5021-96P166.end1.fastq.gz AT1G80840_B_oleracea_TO1000DH3_DAPi711A11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G80840_B_oleracea_TO1000DH3_DAPi711A11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT1G80840_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P220.end1.fastq.gz AT1G80840_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G80840_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01060_B_oleracea_TO1000DH3_DAPi712F05-ORGi5021-96P220.end1.fastq.gz AT2G01060_B_oleracea_TO1000DH3_DAPi712F05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01060_B_oleracea_TO1000DH3_DAPi712F05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01930_B_oleracea_TO1000DH3_DAPi709D06-ORGi5021-96P169.end1.fastq.gz AT2G01930_B_oleracea_TO1000DH3_DAPi709D06-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01930_B_oleracea_TO1000DH3_DAPi709D06-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01930_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P220.end1.fastq.gz AT2G01930_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01930_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01940_B_oleracea_TO1000DH3_DAPi710C09-ORGi5021-96P151.end1.fastq.gz AT2G01940_B_oleracea_TO1000DH3_DAPi710C09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01940_B_oleracea_TO1000DH3_DAPi710C09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G01940_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P220.end1.fastq.gz AT2G01940_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01940_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G02820_B_oleracea_TO1000DH3_DAPi710B09-ORGi5021-96P151.end1.fastq.gz AT2G02820_B_oleracea_TO1000DH3_DAPi710B09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G02820_B_oleracea_TO1000DH3_DAPi710B09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G02820_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P220.end1.fastq.gz AT2G02820_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G02820_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G03500_B_oleracea_TO1000DH3_DAPi711H07-ORGi5021-96P166.end1.fastq.gz AT2G03500_B_oleracea_TO1000DH3_DAPi711H07-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G03500_B_oleracea_TO1000DH3_DAPi711H07-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G15740_B_oleracea_TO1000DH3_DAPi710F08-ORGi5021-96P151.end1.fastq.gz AT2G15740_B_oleracea_TO1000DH3_DAPi710F08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G15740_B_oleracea_TO1000DH3_DAPi710F08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G18380_B_oleracea_TO1000DH3_DAPi710H06-ORGi5021-96P151.end1.fastq.gz AT2G18380_B_oleracea_TO1000DH3_DAPi710H06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G18380_B_oleracea_TO1000DH3_DAPi710H06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G18550_B_oleracea_TO1000DH3_DAPi710E06-ORGi5021-96P151.end1.fastq.gz AT2G18550_B_oleracea_TO1000DH3_DAPi710E06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G18550_B_oleracea_TO1000DH3_DAPi710E06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G18550_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P220.end1.fastq.gz AT2G18550_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G18550_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G20400_B_oleracea_TO1000DH3_DAPi709E09-ORGi5021-96P169.end1.fastq.gz AT2G20400_B_oleracea_TO1000DH3_DAPi709E09-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G20400_B_oleracea_TO1000DH3_DAPi709E09-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G22430_B_oleracea_TO1000DH3_DAPi711F07-ORGi5021-96P166.end1.fastq.gz AT2G22430_B_oleracea_TO1000DH3_DAPi711F07-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G22430_B_oleracea_TO1000DH3_DAPi711F07-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G22430_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P220.end1.fastq.gz AT2G22430_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G22430_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G23290_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P155.end1.fastq.gz AT2G23290_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G23290_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G23320_B_oleracea_TO1000DH3_DAPi711E01-ORGi5021-96P166.end1.fastq.gz AT2G23320_B_oleracea_TO1000DH3_DAPi711E01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G23320_B_oleracea_TO1000DH3_DAPi711E01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G23340_B_oleracea_TO1000DH3_DAPi711E08-ORGi5021-96P166.end1.fastq.gz AT2G23340_B_oleracea_TO1000DH3_DAPi711E08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G23340_B_oleracea_TO1000DH3_DAPi711E08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G24430_B_oleracea_TO1000DH3_DAPi709B10-ORGi5021-96P169.end1.fastq.gz AT2G24430_B_oleracea_TO1000DH3_DAPi709B10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G24430_B_oleracea_TO1000DH3_DAPi709B10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G26960_B_oleracea_TO1000DH3_DAPi710D11-ORGi5021-96P151.end1.fastq.gz AT2G26960_B_oleracea_TO1000DH3_DAPi710D11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G26960_B_oleracea_TO1000DH3_DAPi710D11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G28810_B_oleracea_TO1000DH3_DAPi710A06-ORGi5021-96P151.end1.fastq.gz AT2G28810_B_oleracea_TO1000DH3_DAPi710A06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G28810_B_oleracea_TO1000DH3_DAPi710A06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G30250_B_oleracea_TO1000DH3_DAPi711B11-ORGi5021-96P166.end1.fastq.gz AT2G30250_B_oleracea_TO1000DH3_DAPi711B11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G30250_B_oleracea_TO1000DH3_DAPi711B11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G30250_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P220.end1.fastq.gz AT2G30250_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G30250_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G30340_B_oleracea_TO1000DH3_DAPi710H03-ORGi5021-96P151.end1.fastq.gz AT2G30340_B_oleracea_TO1000DH3_DAPi710H03-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G30340_B_oleracea_TO1000DH3_DAPi710H03-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G31230_B_oleracea_TO1000DH3_DAPi711G02-ORGi5021-96P166.end1.fastq.gz AT2G31230_B_oleracea_TO1000DH3_DAPi711G02-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G31230_B_oleracea_TO1000DH3_DAPi711G02-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G32460_B_oleracea_TO1000DH3_DAPi709G05-ORGi5021-96P169.end1.fastq.gz AT2G32460_B_oleracea_TO1000DH3_DAPi709G05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G32460_B_oleracea_TO1000DH3_DAPi709G05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G33550_B_oleracea_TO1000DH3_DAPi710F01-ORGi5021-96P151.end1.fastq.gz AT2G33550_B_oleracea_TO1000DH3_DAPi710F01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G33550_B_oleracea_TO1000DH3_DAPi710F01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G35530_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P155.end1.fastq.gz AT2G35530_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G35530_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G37590_B_oleracea_TO1000DH3_DAPi710E09-ORGi5021-96P151.end1.fastq.gz AT2G37590_B_oleracea_TO1000DH3_DAPi710E09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G37590_B_oleracea_TO1000DH3_DAPi710E09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G40260_B_oleracea_TO1000DH3_DAPi709C12-ORGi5021-96P169.end1.fastq.gz AT2G40260_B_oleracea_TO1000DH3_DAPi709C12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G40260_B_oleracea_TO1000DH3_DAPi709C12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G40620_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P220.end1.fastq.gz AT2G40620_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G40620_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G40740_B_oleracea_TO1000DH3_DAPi710C11-ORGi5021-96P151.end1.fastq.gz AT2G40740_B_oleracea_TO1000DH3_DAPi710C11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G40740_B_oleracea_TO1000DH3_DAPi710C11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G42430_B_oleracea_TO1000DH3_DAPi710E01-ORGi5021-96P151.end1.fastq.gz AT2G42430_B_oleracea_TO1000DH3_DAPi710E01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G42430_B_oleracea_TO1000DH3_DAPi710E01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G44940_B_oleracea_TO1000DH3_DAPi709F02-ORGi5021-96P169.end1.fastq.gz AT2G44940_B_oleracea_TO1000DH3_DAPi709F02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G44940_B_oleracea_TO1000DH3_DAPi709F02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45410_B_oleracea_TO1000DH3_DAPi710B02-ORGi5021-96P151.end1.fastq.gz AT2G45410_B_oleracea_TO1000DH3_DAPi710B02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45410_B_oleracea_TO1000DH3_DAPi710B02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45420_B_oleracea_TO1000DH3_DAPi712F06-ORGi5021-96P220.end1.fastq.gz AT2G45420_B_oleracea_TO1000DH3_DAPi712F06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45420_B_oleracea_TO1000DH3_DAPi712F06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45480_B_oleracea_TO1000DH3_DAPi710G11-ORGi5021-96P151.end1.fastq.gz AT2G45480_B_oleracea_TO1000DH3_DAPi710G11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45480_B_oleracea_TO1000DH3_DAPi710G11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G45480_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P220.end1.fastq.gz AT2G45480_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45480_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G46270_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P220.end1.fastq.gz AT2G46270_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46270_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G46590_B_oleracea_TO1000DH3_DAPi711B10-ORGi5021-96P166.end1.fastq.gz AT2G46590_B_oleracea_TO1000DH3_DAPi711B10-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46590_B_oleracea_TO1000DH3_DAPi711B10-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G46680_B_oleracea_TO1000DH3_DAPi711E11-ORGi5021-96P166.end1.fastq.gz AT2G46680_B_oleracea_TO1000DH3_DAPi711E11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46680_B_oleracea_TO1000DH3_DAPi711E11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G46770_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P155.end1.fastq.gz AT2G46770_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46770_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G47070_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P155.end1.fastq.gz AT2G47070_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G47070_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT2G47070_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P220.end1.fastq.gz AT2G47070_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G47070_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G01220_B_oleracea_TO1000DH3_DAPi709F01-ORGi5021-96P169.end1.fastq.gz AT3G01220_B_oleracea_TO1000DH3_DAPi709F01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G01220_B_oleracea_TO1000DH3_DAPi709F01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G01530_B_oleracea_TO1000DH3_DAPi711A05-ORGi5021-96P166.end1.fastq.gz AT3G01530_B_oleracea_TO1000DH3_DAPi711A05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G01530_B_oleracea_TO1000DH3_DAPi711A05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G01970_B_oleracea_TO1000DH3_DAPi709C04-ORGi5021-96P169.end1.fastq.gz AT3G01970_B_oleracea_TO1000DH3_DAPi709C04-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G01970_B_oleracea_TO1000DH3_DAPi709C04-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G02940_B_oleracea_TO1000DH3_DAPi709C05-ORGi5021-96P169.end1.fastq.gz AT3G02940_B_oleracea_TO1000DH3_DAPi709C05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G02940_B_oleracea_TO1000DH3_DAPi709C05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G02940_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P220.end1.fastq.gz AT3G02940_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G02940_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G03200_B_oleracea_TO1000DH3_DAPi710A10-ORGi5021-96P151.end1.fastq.gz AT3G03200_B_oleracea_TO1000DH3_DAPi710A10-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G03200_B_oleracea_TO1000DH3_DAPi710A10-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G04030_B_oleracea_TO1000DH3_DAPi711A08-ORGi5021-96P166.end1.fastq.gz AT3G04030_B_oleracea_TO1000DH3_DAPi711A08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G04030_B_oleracea_TO1000DH3_DAPi711A08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G04070_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P155.end1.fastq.gz AT3G04070_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G04070_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G08500_B_oleracea_TO1000DH3_DAPi709F05-ORGi5021-96P169.end1.fastq.gz AT3G08500_B_oleracea_TO1000DH3_DAPi709F05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G08500_B_oleracea_TO1000DH3_DAPi709F05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G08500_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P220.end1.fastq.gz AT3G08500_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G08500_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G09600_B_oleracea_TO1000DH3_DAPi709A02-ORGi5021-96P169.end1.fastq.gz AT3G09600_B_oleracea_TO1000DH3_DAPi709A02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G09600_B_oleracea_TO1000DH3_DAPi709A02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G10030_B_oleracea_TO1000DH3_DAPi710G03-ORGi5021-96P151.end1.fastq.gz AT3G10030_B_oleracea_TO1000DH3_DAPi710G03-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G10030_B_oleracea_TO1000DH3_DAPi710G03-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G10113_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P155.end1.fastq.gz AT3G10113_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G10113_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G10580_B_oleracea_TO1000DH3_DAPi710C01-ORGi5021-96P151.end1.fastq.gz AT3G10580_B_oleracea_TO1000DH3_DAPi710C01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G10580_B_oleracea_TO1000DH3_DAPi710C01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G11280_B_oleracea_TO1000DH3_DAPi709C06-ORGi5021-96P169.end1.fastq.gz AT3G11280_B_oleracea_TO1000DH3_DAPi709C06-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G11280_B_oleracea_TO1000DH3_DAPi709C06-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G12250_B_oleracea_TO1000DH3_DAPi710E03-ORGi5021-96P151.end1.fastq.gz AT3G12250_B_oleracea_TO1000DH3_DAPi710E03-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G12250_B_oleracea_TO1000DH3_DAPi710E03-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G12250_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P220.end1.fastq.gz AT3G12250_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G12250_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G12730_B_oleracea_TO1000DH3_DAPi711B08-ORGi5021-96P166.end1.fastq.gz AT3G12730_B_oleracea_TO1000DH3_DAPi711B08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G12730_B_oleracea_TO1000DH3_DAPi711B08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G14180_B_oleracea_TO1000DH3_DAPi711D03-ORGi5021-96P166.end1.fastq.gz AT3G14180_B_oleracea_TO1000DH3_DAPi711D03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G14180_B_oleracea_TO1000DH3_DAPi711D03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G15170_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P155.end1.fastq.gz AT3G15170_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G15170_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G15210_B_oleracea_TO1000DH3_DAPi711D10-ORGi5021-96P166.end1.fastq.gz AT3G15210_B_oleracea_TO1000DH3_DAPi711D10-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G15210_B_oleracea_TO1000DH3_DAPi711D10-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G15270_B_oleracea_TO1000DH3_DAPi711F08-ORGi5021-96P166.end1.fastq.gz AT3G15270_B_oleracea_TO1000DH3_DAPi711F08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G15270_B_oleracea_TO1000DH3_DAPi711F08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G15500_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P155.end1.fastq.gz AT3G15500_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G15500_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G16280_B_oleracea_TO1000DH3_DAPi709E11-ORGi5021-96P169.end1.fastq.gz AT3G16280_B_oleracea_TO1000DH3_DAPi709E11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G16280_B_oleracea_TO1000DH3_DAPi709E11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G17730_B_oleracea_TO1000DH3_DAPi710C06-ORGi5021-96P151.end1.fastq.gz AT3G17730_B_oleracea_TO1000DH3_DAPi710C06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G17730_B_oleracea_TO1000DH3_DAPi710C06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G18400_B_oleracea_TO1000DH3_DAPi709C10-ORGi5021-96P169.end1.fastq.gz AT3G18400_B_oleracea_TO1000DH3_DAPi709C10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G18400_B_oleracea_TO1000DH3_DAPi709C10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G18990_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P155.end1.fastq.gz AT3G18990_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G18990_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G18990_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P220.end1.fastq.gz AT3G18990_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G18990_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G20310_B_oleracea_TO1000DH3_DAPi711F06-ORGi5021-96P166.end1.fastq.gz AT3G20310_B_oleracea_TO1000DH3_DAPi711F06-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G20310_B_oleracea_TO1000DH3_DAPi711F06-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G20770_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P155.end1.fastq.gz AT3G20770_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G20770_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G22830_B_oleracea_TO1000DH3_DAPi711G01-ORGi5021-96P166.end1.fastq.gz AT3G22830_B_oleracea_TO1000DH3_DAPi711G01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G22830_B_oleracea_TO1000DH3_DAPi711G01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G24050_B_oleracea_TO1000DH3_DAPi709H10-ORGi5021-96P169.end1.fastq.gz AT3G24050_B_oleracea_TO1000DH3_DAPi709H10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G24050_B_oleracea_TO1000DH3_DAPi709H10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G24120_B_oleracea_TO1000DH3_DAPi711B06-ORGi5021-96P166.end1.fastq.gz AT3G24120_B_oleracea_TO1000DH3_DAPi711B06-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G24120_B_oleracea_TO1000DH3_DAPi711B06-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G25990_B_oleracea_TO1000DH3_DAPi710H05-ORGi5021-96P151.end1.fastq.gz AT3G25990_B_oleracea_TO1000DH3_DAPi710H05-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G25990_B_oleracea_TO1000DH3_DAPi710H05-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G27010_B_oleracea_TO1000DH3_DAPi709C02-ORGi5021-96P169.end1.fastq.gz AT3G27010_B_oleracea_TO1000DH3_DAPi709C02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G27010_B_oleracea_TO1000DH3_DAPi709C02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G27010_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P220.end1.fastq.gz AT3G27010_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G27010_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G28920_B_oleracea_TO1000DH3_DAPi709A08-ORGi5021-96P169.end1.fastq.gz AT3G28920_B_oleracea_TO1000DH3_DAPi709A08-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G28920_B_oleracea_TO1000DH3_DAPi709A08-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G30210_B_oleracea_TO1000DH3_DAPi710C02-ORGi5021-96P151.end1.fastq.gz AT3G30210_B_oleracea_TO1000DH3_DAPi710C02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G30210_B_oleracea_TO1000DH3_DAPi710C02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G46590_B_oleracea_TO1000DH3_DAPi710D06-ORGi5021-96P151.end1.fastq.gz AT3G46590_B_oleracea_TO1000DH3_DAPi710D06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G46590_B_oleracea_TO1000DH3_DAPi710D06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G49530_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P155.end1.fastq.gz AT3G49530_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G49530_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50060_B_oleracea_TO1000DH3_DAPi711D07-ORGi5021-96P166.end1.fastq.gz AT3G50060_B_oleracea_TO1000DH3_DAPi711D07-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50060_B_oleracea_TO1000DH3_DAPi711D07-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50060_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P220.end1.fastq.gz AT3G50060_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50060_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50260_B_oleracea_TO1000DH3_DAPi711D06-ORGi5021-96P166.end1.fastq.gz AT3G50260_B_oleracea_TO1000DH3_DAPi711D06-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50260_B_oleracea_TO1000DH3_DAPi711D06-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50260_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P220.end1.fastq.gz AT3G50260_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50260_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50410_B_oleracea_TO1000DH3_DAPi710B03-ORGi5021-96P151.end1.fastq.gz AT3G50410_B_oleracea_TO1000DH3_DAPi710B03-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50410_B_oleracea_TO1000DH3_DAPi710B03-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G50410_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P220.end1.fastq.gz AT3G50410_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50410_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G52440_B_oleracea_TO1000DH3_DAPi709B11-ORGi5021-96P169.end1.fastq.gz AT3G52440_B_oleracea_TO1000DH3_DAPi709B11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G52440_B_oleracea_TO1000DH3_DAPi709B11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G55370_B_oleracea_TO1000DH3_DAPi710H10-ORGi5021-96P151.end1.fastq.gz AT3G55370_B_oleracea_TO1000DH3_DAPi710H10-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G55370_B_oleracea_TO1000DH3_DAPi710H10-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G56400_B_oleracea_TO1000DH3_DAPi711A04-ORGi5021-96P166.end1.fastq.gz AT3G56400_B_oleracea_TO1000DH3_DAPi711A04-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G56400_B_oleracea_TO1000DH3_DAPi711A04-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G56400_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P220.end1.fastq.gz AT3G56400_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G56400_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G56850_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P155.end1.fastq.gz AT3G56850_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G56850_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G57920_B_oleracea_TO1000DH3_DAPi709E12-ORGi5021-96P169.end1.fastq.gz AT3G57920_B_oleracea_TO1000DH3_DAPi709E12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G57920_B_oleracea_TO1000DH3_DAPi709E12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G57920_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P220.end1.fastq.gz AT3G57920_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G57920_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G60490_B_oleracea_TO1000DH3_DAPi710A02-ORGi5021-96P151.end1.fastq.gz AT3G60490_B_oleracea_TO1000DH3_DAPi710A02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G60490_B_oleracea_TO1000DH3_DAPi710A02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G60530_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P220.end1.fastq.gz AT3G60530_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G60530_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT3G62420_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P155.end1.fastq.gz AT3G62420_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G62420_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G00730_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P220.end1.fastq.gz AT4G00730_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G00730_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G00730_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P155.end1.fastq.gz AT4G00730_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G00730_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G01250_B_oleracea_TO1000DH3_DAPi711A02-ORGi5021-96P166.end1.fastq.gz AT4G01250_B_oleracea_TO1000DH3_DAPi711A02-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G01250_B_oleracea_TO1000DH3_DAPi711A02-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G01280_B_oleracea_TO1000DH3_DAPi709E03-ORGi5021-96P169.end1.fastq.gz AT4G01280_B_oleracea_TO1000DH3_DAPi709E03-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G01280_B_oleracea_TO1000DH3_DAPi709E03-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G01500_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P155.end1.fastq.gz AT4G01500_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G01500_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G01550_B_oleracea_TO1000DH3_DAPi710D08-ORGi5021-96P151.end1.fastq.gz AT4G01550_B_oleracea_TO1000DH3_DAPi710D08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G01550_B_oleracea_TO1000DH3_DAPi710D08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G06746_B_oleracea_TO1000DH3_DAPi709E10-ORGi5021-96P169.end1.fastq.gz AT4G06746_B_oleracea_TO1000DH3_DAPi709E10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G06746_B_oleracea_TO1000DH3_DAPi709E10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G10350_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P155.end1.fastq.gz AT4G10350_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G10350_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G14770_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P155.end1.fastq.gz AT4G14770_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G14770_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G14770_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P220.end1.fastq.gz AT4G14770_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G14770_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G16750_B_oleracea_TO1000DH3_DAPi711E12-ORGi5021-96P166.end1.fastq.gz AT4G16750_B_oleracea_TO1000DH3_DAPi711E12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G16750_B_oleracea_TO1000DH3_DAPi711E12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G17980_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P155.end1.fastq.gz AT4G17980_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G17980_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G17980_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P220.end1.fastq.gz AT4G17980_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G17980_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G18450_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P155.end1.fastq.gz AT4G18450_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G18450_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G21030_B_oleracea_TO1000DH3_DAPi712E02-ORGi5021-96P155.end1.fastq.gz AT4G21030_B_oleracea_TO1000DH3_DAPi712E02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G21030_B_oleracea_TO1000DH3_DAPi712E02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G21080_B_oleracea_TO1000DH3_DAPi710G07-ORGi5021-96P151.end1.fastq.gz AT4G21080_B_oleracea_TO1000DH3_DAPi710G07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G21080_B_oleracea_TO1000DH3_DAPi710G07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G23550_B_oleracea_TO1000DH3_DAPi709E05-ORGi5021-96P169.end1.fastq.gz AT4G23550_B_oleracea_TO1000DH3_DAPi709E05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G23550_B_oleracea_TO1000DH3_DAPi709E05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G24240_B_oleracea_TO1000DH3_DAPi711A03-ORGi5021-96P166.end1.fastq.gz AT4G24240_B_oleracea_TO1000DH3_DAPi711A03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G24240_B_oleracea_TO1000DH3_DAPi711A03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25470_B_oleracea_TO1000DH3_DAPi709D11-ORGi5021-96P169.end1.fastq.gz AT4G25470_B_oleracea_TO1000DH3_DAPi709D11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25470_B_oleracea_TO1000DH3_DAPi709D11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25470_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P220.end1.fastq.gz AT4G25470_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25470_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25480_B_oleracea_TO1000DH3_DAPi709D03-ORGi5021-96P169.end1.fastq.gz AT4G25480_B_oleracea_TO1000DH3_DAPi709D03-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25480_B_oleracea_TO1000DH3_DAPi709D03-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25480_B_oleracea_TO1000DH3_DAPi712F04-ORGi5021-96P220.end1.fastq.gz AT4G25480_B_oleracea_TO1000DH3_DAPi712F04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25480_B_oleracea_TO1000DH3_DAPi712F04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25490_B_oleracea_TO1000DH3_DAPi710E07-ORGi5021-96P151.end1.fastq.gz AT4G25490_B_oleracea_TO1000DH3_DAPi710E07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25490_B_oleracea_TO1000DH3_DAPi710E07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G25490_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P220.end1.fastq.gz AT4G25490_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25490_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G28500_B_oleracea_TO1000DH3_DAPi710E05-ORGi5021-96P151.end1.fastq.gz AT4G28500_B_oleracea_TO1000DH3_DAPi710E05-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G28500_B_oleracea_TO1000DH3_DAPi710E05-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G31060_B_oleracea_TO1000DH3_DAPi709A03-ORGi5021-96P169.end1.fastq.gz AT4G31060_B_oleracea_TO1000DH3_DAPi709A03-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G31060_B_oleracea_TO1000DH3_DAPi709A03-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G31800_B_oleracea_TO1000DH3_DAPi711C07-ORGi5021-96P166.end1.fastq.gz AT4G31800_B_oleracea_TO1000DH3_DAPi711C07-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G31800_B_oleracea_TO1000DH3_DAPi711C07-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G31800_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P220.end1.fastq.gz AT4G31800_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G31800_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G32730_B_oleracea_TO1000DH3_DAPi712C05-ORGi5021-96P155.end1.fastq.gz AT4G32730_B_oleracea_TO1000DH3_DAPi712C05-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G32730_B_oleracea_TO1000DH3_DAPi712C05-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G34410_B_oleracea_TO1000DH3_DAPi711F11-ORGi5021-96P166.end1.fastq.gz AT4G34410_B_oleracea_TO1000DH3_DAPi711F11-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G34410_B_oleracea_TO1000DH3_DAPi711F11-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G34590_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P155.end1.fastq.gz AT4G34590_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G34590_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G36620_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P155.end1.fastq.gz AT4G36620_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G36620_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G36740_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P155.end1.fastq.gz AT4G36740_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G36740_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G36780_B_oleracea_TO1000DH3_DAPi711H06-ORGi5021-96P166.end1.fastq.gz AT4G36780_B_oleracea_TO1000DH3_DAPi711H06-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G36780_B_oleracea_TO1000DH3_DAPi711H06-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT4G38000_B_oleracea_TO1000DH3_DAPi709B02-ORGi5021-96P169.end1.fastq.gz AT4G38000_B_oleracea_TO1000DH3_DAPi709B02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G38000_B_oleracea_TO1000DH3_DAPi709B02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G02320_B_oleracea_TO1000DH3_DAPi710G02-ORGi5021-96P151.end1.fastq.gz AT5G02320_B_oleracea_TO1000DH3_DAPi710G02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02320_B_oleracea_TO1000DH3_DAPi710G02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G02320_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P220.end1.fastq.gz AT5G02320_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02320_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G02460_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P155.end1.fastq.gz AT5G02460_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02460_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G02840_B_oleracea_TO1000DH3_DAPi709E07-ORGi5021-96P169.end1.fastq.gz AT5G02840_B_oleracea_TO1000DH3_DAPi709E07-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02840_B_oleracea_TO1000DH3_DAPi709E07-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03150_B_oleracea_TO1000DH3_DAPi710E08-ORGi5021-96P151.end1.fastq.gz AT5G03150_B_oleracea_TO1000DH3_DAPi710E08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03150_B_oleracea_TO1000DH3_DAPi710E08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03150_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P220.end1.fastq.gz AT5G03150_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03150_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03790_B_oleracea_TO1000DH3_DAPi709B12-ORGi5021-96P169.end1.fastq.gz AT5G03790_B_oleracea_TO1000DH3_DAPi709B12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03790_B_oleracea_TO1000DH3_DAPi709B12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G03790_B_oleracea_TO1000DH3_DAPi712C06-ORGi5021-96P220.end1.fastq.gz AT5G03790_B_oleracea_TO1000DH3_DAPi712C06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03790_B_oleracea_TO1000DH3_DAPi712C06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G05550_B_oleracea_TO1000DH3_DAPi710G12-ORGi5021-96P151.end1.fastq.gz AT5G05550_B_oleracea_TO1000DH3_DAPi710G12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G05550_B_oleracea_TO1000DH3_DAPi710G12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G05550_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P220.end1.fastq.gz AT5G05550_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G05550_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G05790_B_oleracea_TO1000DH3_DAPi711G12-ORGi5021-96P166.end1.fastq.gz AT5G05790_B_oleracea_TO1000DH3_DAPi711G12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G05790_B_oleracea_TO1000DH3_DAPi711G12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G06100_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P155.end1.fastq.gz AT5G06100_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G06100_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G07310_B_oleracea_TO1000DH3_DAPi709A05-ORGi5021-96P169.end1.fastq.gz AT5G07310_B_oleracea_TO1000DH3_DAPi709A05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G07310_B_oleracea_TO1000DH3_DAPi709A05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G07680_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P155.end1.fastq.gz AT5G07680_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G07680_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G08130_B_oleracea_TO1000DH3_DAPi709H05-ORGi5021-96P169.end1.fastq.gz AT5G08130_B_oleracea_TO1000DH3_DAPi709H05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G08130_B_oleracea_TO1000DH3_DAPi709H05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G08330_B_oleracea_TO1000DH3_DAPi711E05-ORGi5021-96P166.end1.fastq.gz AT5G08330_B_oleracea_TO1000DH3_DAPi711E05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G08330_B_oleracea_TO1000DH3_DAPi711E05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G08520_B_oleracea_TO1000DH3_DAPi711E02-ORGi5021-96P166.end1.fastq.gz AT5G08520_B_oleracea_TO1000DH3_DAPi711E02-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G08520_B_oleracea_TO1000DH3_DAPi711E02-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G09410_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P155.end1.fastq.gz AT5G09410_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G09410_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G09410_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P220.end1.fastq.gz AT5G09410_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G09410_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G10030_B_oleracea_TO1000DH3_DAPi709C11-ORGi5021-96P169.end1.fastq.gz AT5G10030_B_oleracea_TO1000DH3_DAPi709C11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G10030_B_oleracea_TO1000DH3_DAPi709C11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G10030_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P220.end1.fastq.gz AT5G10030_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G10030_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G11260_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P220.end1.fastq.gz AT5G11260_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G11260_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G11260_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P155.end1.fastq.gz AT5G11260_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G11260_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G11510_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P155.end1.fastq.gz AT5G11510_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G11510_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G13080_B_oleracea_TO1000DH3_DAPi711B12-ORGi5021-96P166.end1.fastq.gz AT5G13080_B_oleracea_TO1000DH3_DAPi711B12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G13080_B_oleracea_TO1000DH3_DAPi711B12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G13790_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P155.end1.fastq.gz AT5G13790_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G13790_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G13910_B_oleracea_TO1000DH3_DAPi709A04-ORGi5021-96P169.end1.fastq.gz AT5G13910_B_oleracea_TO1000DH3_DAPi709A04-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G13910_B_oleracea_TO1000DH3_DAPi709A04-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G14960_B_oleracea_TO1000DH3_DAPi710G08-ORGi5021-96P151.end1.fastq.gz AT5G14960_B_oleracea_TO1000DH3_DAPi710G08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G14960_B_oleracea_TO1000DH3_DAPi710G08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G14960_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P220.end1.fastq.gz AT5G14960_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G14960_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G16820_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P155.end1.fastq.gz AT5G16820_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G16820_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G17300_B_oleracea_TO1000DH3_DAPi710F09-ORGi5021-96P151.end1.fastq.gz AT5G17300_B_oleracea_TO1000DH3_DAPi710F09-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G17300_B_oleracea_TO1000DH3_DAPi710F09-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G17300_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P220.end1.fastq.gz AT5G17300_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G17300_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G17800_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P155.end1.fastq.gz AT5G17800_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G17800_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G18270_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P155.end1.fastq.gz AT5G18270_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G18270_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G18560_B_oleracea_TO1000DH3_DAPi710D07-ORGi5021-96P151.end1.fastq.gz AT5G18560_B_oleracea_TO1000DH3_DAPi710D07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G18560_B_oleracea_TO1000DH3_DAPi710D07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G18560_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P220.end1.fastq.gz AT5G18560_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G18560_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G19790_B_oleracea_TO1000DH3_DAPi710A07-ORGi5021-96P151.end1.fastq.gz AT5G19790_B_oleracea_TO1000DH3_DAPi710A07-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G19790_B_oleracea_TO1000DH3_DAPi710A07-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G19790_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P220.end1.fastq.gz AT5G19790_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G19790_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G22990_B_oleracea_TO1000DH3_DAPi710F02-ORGi5021-96P151.end1.fastq.gz AT5G22990_B_oleracea_TO1000DH3_DAPi710F02-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G22990_B_oleracea_TO1000DH3_DAPi710F02-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G24110_B_oleracea_TO1000DH3_DAPi711B09-ORGi5021-96P166.end1.fastq.gz AT5G24110_B_oleracea_TO1000DH3_DAPi711B09-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G24110_B_oleracea_TO1000DH3_DAPi711B09-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G25190_B_oleracea_TO1000DH3_DAPi711C05-ORGi5021-96P166.end1.fastq.gz AT5G25190_B_oleracea_TO1000DH3_DAPi711C05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G25190_B_oleracea_TO1000DH3_DAPi711C05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G25810_B_oleracea_TO1000DH3_DAPi709E04-ORGi5021-96P169.end1.fastq.gz AT5G25810_B_oleracea_TO1000DH3_DAPi709E04-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G25810_B_oleracea_TO1000DH3_DAPi709E04-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G26170_B_oleracea_TO1000DH3_DAPi710B11-ORGi5021-96P151.end1.fastq.gz AT5G26170_B_oleracea_TO1000DH3_DAPi710B11-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G26170_B_oleracea_TO1000DH3_DAPi710B11-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G39610_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P155.end1.fastq.gz AT5G39610_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G39610_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G39760_B_oleracea_TO1000DH3_DAPi711G03-ORGi5021-96P166.end1.fastq.gz AT5G39760_B_oleracea_TO1000DH3_DAPi711G03-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G39760_B_oleracea_TO1000DH3_DAPi711G03-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G39760_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P220.end1.fastq.gz AT5G39760_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G39760_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G41570_B_oleracea_TO1000DH3_DAPi711G08-ORGi5021-96P166.end1.fastq.gz AT5G41570_B_oleracea_TO1000DH3_DAPi711G08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G41570_B_oleracea_TO1000DH3_DAPi711G08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G45300_B_oleracea_TO1000DH3_DAPi712D04-ORGi5021-96P155.end1.fastq.gz AT5G45300_B_oleracea_TO1000DH3_DAPi712D04-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G45300_B_oleracea_TO1000DH3_DAPi712D04-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G45300_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P220.end1.fastq.gz AT5G45300_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G45300_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G45580_B_oleracea_TO1000DH3_DAPi709A11-ORGi5021-96P169.end1.fastq.gz AT5G45580_B_oleracea_TO1000DH3_DAPi709A11-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G45580_B_oleracea_TO1000DH3_DAPi709A11-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47230_B_oleracea_TO1000DH3_DAPi709G06-ORGi5021-96P169.end1.fastq.gz AT5G47230_B_oleracea_TO1000DH3_DAPi709G06-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47230_B_oleracea_TO1000DH3_DAPi709G06-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47370_B_oleracea_TO1000DH3_DAPi711B05-ORGi5021-96P166.end1.fastq.gz AT5G47370_B_oleracea_TO1000DH3_DAPi711B05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47370_B_oleracea_TO1000DH3_DAPi711B05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47390_B_oleracea_TO1000DH3_DAPi711H02-ORGi5021-96P166.end1.fastq.gz AT5G47390_B_oleracea_TO1000DH3_DAPi711H02-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47390_B_oleracea_TO1000DH3_DAPi711H02-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47390_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P220.end1.fastq.gz AT5G47390_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47390_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G47660_B_oleracea_TO1000DH3_DAPi710B06-ORGi5021-96P151.end1.fastq.gz AT5G47660_B_oleracea_TO1000DH3_DAPi710B06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47660_B_oleracea_TO1000DH3_DAPi710B06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G51190_B_oleracea_TO1000DH3_DAPi709G07-ORGi5021-96P169.end1.fastq.gz AT5G51190_B_oleracea_TO1000DH3_DAPi709G07-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G51190_B_oleracea_TO1000DH3_DAPi709G07-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G51990_B_oleracea_TO1000DH3_DAPi710C04-ORGi5021-96P151.end1.fastq.gz AT5G51990_B_oleracea_TO1000DH3_DAPi710C04-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G51990_B_oleracea_TO1000DH3_DAPi710C04-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G52020_B_oleracea_TO1000DH3_DAPi709A10-ORGi5021-96P169.end1.fastq.gz AT5G52020_B_oleracea_TO1000DH3_DAPi709A10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52020_B_oleracea_TO1000DH3_DAPi709A10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G52660_B_oleracea_TO1000DH3_DAPi709A06-ORGi5021-96P169.end1.fastq.gz AT5G52660_B_oleracea_TO1000DH3_DAPi709A06-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52660_B_oleracea_TO1000DH3_DAPi709A06-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G52830_B_oleracea_TO1000DH3_DAPi710G06-ORGi5021-96P151.end1.fastq.gz AT5G52830_B_oleracea_TO1000DH3_DAPi710G06-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52830_B_oleracea_TO1000DH3_DAPi710G06-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G52830_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P220.end1.fastq.gz AT5G52830_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52830_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G53950_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P155.end1.fastq.gz AT5G53950_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G53950_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G54230_B_oleracea_TO1000DH3_DAPi709D07-ORGi5021-96P169.end1.fastq.gz AT5G54230_B_oleracea_TO1000DH3_DAPi709D07-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G54230_B_oleracea_TO1000DH3_DAPi709D07-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G56110_B_oleracea_TO1000DH3_DAPi709F12-ORGi5021-96P169.end1.fastq.gz AT5G56110_B_oleracea_TO1000DH3_DAPi709F12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G56110_B_oleracea_TO1000DH3_DAPi709F12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G56110_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P220.end1.fastq.gz AT5G56110_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G56110_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G56840_B_oleracea_TO1000DH3_DAPi710D01-ORGi5021-96P151.end1.fastq.gz AT5G56840_B_oleracea_TO1000DH3_DAPi710D01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G56840_B_oleracea_TO1000DH3_DAPi710D01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G57620_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P155.end1.fastq.gz AT5G57620_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G57620_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G58850_B_oleracea_TO1000DH3_DAPi710A05-ORGi5021-96P151.end1.fastq.gz AT5G58850_B_oleracea_TO1000DH3_DAPi710A05-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G58850_B_oleracea_TO1000DH3_DAPi710A05-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G58900_B_oleracea_TO1000DH3_DAPi711H04-ORGi5021-96P166.end1.fastq.gz AT5G58900_B_oleracea_TO1000DH3_DAPi711H04-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G58900_B_oleracea_TO1000DH3_DAPi711H04-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G60130_B_oleracea_TO1000DH3_DAPi710A04-ORGi5021-96P151.end1.fastq.gz AT5G60130_B_oleracea_TO1000DH3_DAPi710A04-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G60130_B_oleracea_TO1000DH3_DAPi710A04-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G60130_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P220.end1.fastq.gz AT5G60130_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G60130_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G60850_B_oleracea_TO1000DH3_DAPi711F05-ORGi5021-96P166.end1.fastq.gz AT5G60850_B_oleracea_TO1000DH3_DAPi711F05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G60850_B_oleracea_TO1000DH3_DAPi711F05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G61620_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P155.end1.fastq.gz AT5G61620_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G61620_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62000_B_oleracea_TO1000DH3_DAPi711D08-ORGi5021-96P166.end1.fastq.gz AT5G62000_B_oleracea_TO1000DH3_DAPi711D08-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62000_B_oleracea_TO1000DH3_DAPi711D08-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62020_B_oleracea_TO1000DH3_DAPi709G02-ORGi5021-96P169.end1.fastq.gz AT5G62020_B_oleracea_TO1000DH3_DAPi709G02-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62020_B_oleracea_TO1000DH3_DAPi709G02-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62020_B_oleracea_TO1000DH3_DAPi712E04-ORGi5021-96P220.end1.fastq.gz AT5G62020_B_oleracea_TO1000DH3_DAPi712E04-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62020_B_oleracea_TO1000DH3_DAPi712E04-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62320_B_oleracea_TO1000DH3_DAPi710A03-ORGi5021-96P151.end1.fastq.gz AT5G62320_B_oleracea_TO1000DH3_DAPi710A03-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62320_B_oleracea_TO1000DH3_DAPi710A03-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62470_B_oleracea_TO1000DH3_DAPi710A08-ORGi5021-96P151.end1.fastq.gz AT5G62470_B_oleracea_TO1000DH3_DAPi710A08-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62470_B_oleracea_TO1000DH3_DAPi710A08-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62470_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P220.end1.fastq.gz AT5G62470_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62470_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62940_B_oleracea_TO1000DH3_DAPi709D05-ORGi5021-96P169.end1.fastq.gz AT5G62940_B_oleracea_TO1000DH3_DAPi709D05-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62940_B_oleracea_TO1000DH3_DAPi709D05-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G62940_B_oleracea_TO1000DH3_DAPi712A05-ORGi5021-96P220.end1.fastq.gz AT5G62940_B_oleracea_TO1000DH3_DAPi712A05-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62940_B_oleracea_TO1000DH3_DAPi712A05-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G64060_B_oleracea_TO1000DH3_DAPi709F10-ORGi5021-96P169.end1.fastq.gz AT5G64060_B_oleracea_TO1000DH3_DAPi709F10-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G64060_B_oleracea_TO1000DH3_DAPi709F10-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G64750_B_oleracea_TO1000DH3_DAPi711G09-ORGi5021-96P166.end1.fastq.gz AT5G64750_B_oleracea_TO1000DH3_DAPi711G09-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G64750_B_oleracea_TO1000DH3_DAPi711G09-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G64750_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P220.end1.fastq.gz AT5G64750_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G64750_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65130_B_oleracea_TO1000DH3_DAPi709B01-ORGi5021-96P169.end1.fastq.gz AT5G65130_B_oleracea_TO1000DH3_DAPi709B01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65130_B_oleracea_TO1000DH3_DAPi709B01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65210_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P155.end1.fastq.gz AT5G65210_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65210_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65310_B_oleracea_TO1000DH3_DAPi710G10-ORGi5021-96P151.end1.fastq.gz AT5G65310_B_oleracea_TO1000DH3_DAPi710G10-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65310_B_oleracea_TO1000DH3_DAPi710G10-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65410_B_oleracea_TO1000DH3_DAPi711D09-ORGi5021-96P166.end1.fastq.gz AT5G65410_B_oleracea_TO1000DH3_DAPi711D09-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65410_B_oleracea_TO1000DH3_DAPi711D09-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G65410_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P220.end1.fastq.gz AT5G65410_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65410_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G66300_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P155.end1.fastq.gz AT5G66300_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G66300_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G66700_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P155.end1.fastq.gz AT5G66700_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G66700_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G66940_B_oleracea_TO1000DH3_DAPi710B10-ORGi5021-96P151.end1.fastq.gz AT5G66940_B_oleracea_TO1000DH3_DAPi710B10-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G66940_B_oleracea_TO1000DH3_DAPi710B10-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G67300_B_oleracea_TO1000DH3_DAPi711B01-ORGi5021-96P166.end1.fastq.gz AT5G67300_B_oleracea_TO1000DH3_DAPi711B01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G67300_B_oleracea_TO1000DH3_DAPi711B01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G67300_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P220.end1.fastq.gz AT5G67300_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G67300_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AT5G67580_B_oleracea_TO1000DH3_DAPi711D05-ORGi5021-96P166.end1.fastq.gz AT5G67580_B_oleracea_TO1000DH3_DAPi711D05-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G67580_B_oleracea_TO1000DH3_DAPi711D05-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s0116.1_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P247.end1.fastq.gz Carub.0001s0116.1_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s0116.1_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s1194.1_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P247.end1.fastq.gz Carub.0001s1194.1_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s1194.1_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0001s3581.1.p_B_oleracea_TO1000DH3_DAPi712D01-ORGi5021-96P247.end1.fastq.gz Carub.0001s3581.1.p_B_oleracea_TO1000DH3_DAPi712D01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s3581.1.p_B_oleracea_TO1000DH3_DAPi712D01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s1646.1_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P247.end1.fastq.gz Carub.0002s1646.1_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1646.1_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s1959.1_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P247.end1.fastq.gz Carub.0002s1959.1_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1959.1_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0002s2670.1_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P247.end1.fastq.gz Carub.0002s2670.1_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s2670.1_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0003s1161.1.p_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P247.end1.fastq.gz Carub.0003s1161.1.p_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0003s1161.1.p_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0004s2291.1_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P247.end1.fastq.gz Carub.0004s2291.1_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2291.1_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0004s2898.1.p_B_oleracea_TO1000DH3_DAPi712B07-ORGi5021-96P247.end1.fastq.gz Carub.0004s2898.1.p_B_oleracea_TO1000DH3_DAPi712B07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2898.1.p_B_oleracea_TO1000DH3_DAPi712B07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0008s0039.1_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P247.end1.fastq.gz Carub.0008s0039.1_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0039.1_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Carub.0008s0285.1_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P247.end1.fastq.gz Carub.0008s0285.1_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0285.1_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A01-ORGi5021-96P169.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A12-ORGi5021-96P169.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H01-ORGi5021-96P169.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H01-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H01-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H12-ORGi5021-96P169.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H12-ORGi5021-96P169.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H12-ORGi5021-96P169.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A01-ORGi5021-96P166.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A12-ORGi5021-96P166.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H01-ORGi5021-96P166.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H01-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H01-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H12-ORGi5021-96P166.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H12-ORGi5021-96P166.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H12-ORGi5021-96P166.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P220.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P247.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P220.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P247.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P220.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P247.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155-repool.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155-repool.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155-repool.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P220.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P220.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P220.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P247.end1.fastq.gz Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g17260.2_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P247.end1.fastq.gz LOC_Os01g17260.2_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g17260.2_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g18240.1_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P247.end1.fastq.gz LOC_Os01g18240.1_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g18240.1_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g46970.1_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P247.end1.fastq.gz LOC_Os01g46970.1_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g46970.1_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os01g51154.1_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P247.end1.fastq.gz LOC_Os01g51154.1_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g51154.1_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os02g33430.1_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P247.end1.fastq.gz LOC_Os02g33430.1_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g33430.1_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os02g42970.1_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P247.end1.fastq.gz LOC_Os02g42970.1_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g42970.1_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os03g21800.1_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P247.end1.fastq.gz LOC_Os03g21800.1_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os03g21800.1_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os06g07030.1_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P247.end1.fastq.gz LOC_Os06g07030.1_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os06g07030.1_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os08g06110.3_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P247.end1.fastq.gz LOC_Os08g06110.3_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g06110.3_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os08g37970.1_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P247.end1.fastq.gz LOC_Os08g37970.1_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g37970.1_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os09g25060.1_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P247.end1.fastq.gz LOC_Os09g25060.1_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os09g25060.1_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os10g26500.1_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P247.end1.fastq.gz LOC_Os10g26500.1_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g26500.1_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOC_Os10g41200.1_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P247.end1.fastq.gz LOC_Os10g41200.1_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g41200.1_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc01g095460.3.1_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P247.end1.fastq.gz Solyc01g095460.3.1_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g095460.3.1_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc01g102340.3.1_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P247.end1.fastq.gz Solyc01g102340.3.1_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g102340.3.1_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc03g116890.3.1_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P247.end1.fastq.gz Solyc03g116890.3.1_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc03g116890.3.1_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc04g078640.3.1_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P247.end1.fastq.gz Solyc04g078640.3.1_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc04g078640.3.1_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc05g007180.3.1_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P247.end1.fastq.gz Solyc05g007180.3.1_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc05g007180.3.1_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc06g048630.3.1_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P247.end1.fastq.gz Solyc06g048630.3.1_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc06g048630.3.1_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc07g040920.2.1_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P247.end1.fastq.gz Solyc07g040920.2.1_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc07g040920.2.1_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g068320.3.1_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P247.end1.fastq.gz Solyc08g068320.3.1_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g068320.3.1_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g078340.3.1_B_oleracea_TO1000DH3_DAPi712H09-ORGi5021-96P247.end1.fastq.gz Solyc08g078340.3.1_B_oleracea_TO1000DH3_DAPi712H09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g078340.3.1_B_oleracea_TO1000DH3_DAPi712H09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc08g079120.3.1_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P247.end1.fastq.gz Solyc08g079120.3.1_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g079120.3.1_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc10g005080.3.1_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P247.end1.fastq.gz Solyc10g005080.3.1_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc10g005080.3.1_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Solyc11g064950.3.1_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P247.end1.fastq.gz Solyc11g064950.3.1_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc11g064950.3.1_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013586407.1_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P247.end1.fastq.gz XP_013586407.1_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013586407.1_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013587350.1_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P247.end1.fastq.gz XP_013587350.1_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587350.1_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013587997.1_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P247.end1.fastq.gz XP_013587997.1_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587997.1_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013589913.1_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P247.end1.fastq.gz XP_013589913.1_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589913.1_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013589953.1_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P247.end1.fastq.gz XP_013589953.1_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589953.1_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013602769.1_B_oleracea_TO1000DH3_DAPi712C03-ORGi5021-96P247.end1.fastq.gz XP_013602769.1_B_oleracea_TO1000DH3_DAPi712C03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013602769.1_B_oleracea_TO1000DH3_DAPi712C03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013609718.1_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P247.end1.fastq.gz XP_013609718.1_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013609718.1_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013613838.1_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P247.end1.fastq.gz XP_013613838.1_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013613838.1_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013615900.1_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P247.end1.fastq.gz XP_013615900.1_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013615900.1_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013629448.1_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P247.end1.fastq.gz XP_013629448.1_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013629448.1_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013631386.1_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P247.end1.fastq.gz XP_013631386.1_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631386.1_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013631649.1_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P247.end1.fastq.gz XP_013631649.1_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631649.1_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P247.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py XP_013634112.1_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P247.end1.fastq.gz XP_013634112.1_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P247.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/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL -p 20 -v 1 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Brassica_oleracea_var._oleracea-BOL/bowtie-indexes/Brassica_oleracea_var._oleracea-BOL.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013634112.1_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P247.PE.a