python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-14.end1.fastq.gz AP2-14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-14.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-15.end1.fastq.gz AP2-15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-15.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-1.end1.fastq.gz AP2-DREB-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-18.end1.fastq.gz AP2-DREB-18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-18.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-19.end1.fastq.gz AP2-DREB-19.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-19.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-21.end1.fastq.gz AP2-DREB-21.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-21.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-7.end1.fastq.gz AP2-DREB-7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-7.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-8.end1.fastq.gz AP2-DREB-8.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-8.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-DREB-9.end1.fastq.gz AP2-DREB-9.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-DREB-9.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-ERF-13.end1.fastq.gz AP2-ERF-13.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-ERF-13.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-ERF-23.end1.fastq.gz AP2-ERF-23.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-ERF-23.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py AP2-RAV-26.end1.fastq.gz AP2-RAV-26.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2-RAV-26.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py B3-10.end1.fastq.gz B3-10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B3-10.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2C2-1.end1.fastq.gz C2C2-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2C2-1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2C2-2.end1.fastq.gz C2C2-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2C2-2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2C2-3.end1.fastq.gz C2C2-3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2C2-3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2C2-4.end1.fastq.gz C2C2-4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2C2-4.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2C2-5.end1.fastq.gz C2C2-5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2C2-5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C2H2-4.end1.fastq.gz C2H2-4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C2H2-4.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3H-1.end1.fastq.gz C3H-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3H-1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3H-2.end1.fastq.gz C3H-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3H-2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py C3H-5.end1.fastq.gz C3H-5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - C3H-5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GARP-G2-1.end1.fastq.gz GARP-G2-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GARP-G2-1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GARP2.end1.fastq.gz GARP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GARP2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GARP5.end1.fastq.gz GARP5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GARP5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GARP6.end1.fastq.gz GARP6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GARP6.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py GRAS2.end1.fastq.gz GRAS2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - GRAS2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HB-HD-ZIP-2.end1.fastq.gz HB-HD-ZIP-2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HB-HD-ZIP-2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HB-HD-ZIP-3.end1.fastq.gz HB-HD-ZIP-3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HB-HD-ZIP-3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HB-HD-ZIP-6.end1.fastq.gz HB-HD-ZIP-6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HB-HD-ZIP-6.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py HSF1.end1.fastq.gz HSF1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HSF1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Halo_rep1.end1.fastq.gz Halo_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Halo_rep1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Halo_rep2.end1.fastq.gz Halo_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Halo_rep2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Halo_rep3.end1.fastq.gz Halo_rep3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Halo_rep3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOB2.end1.fastq.gz LOB2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOB2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOB3.end1.fastq.gz LOB3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOB3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py LOB5.end1.fastq.gz LOB5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOB5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB11.end1.fastq.gz MYB11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB11.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB12.end1.fastq.gz MYB12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB12.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB13.end1.fastq.gz MYB13.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB13.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB14.end1.fastq.gz MYB14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB14.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB15.end1.fastq.gz MYB15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB15.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB16.end1.fastq.gz MYB16.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB16.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB17.end1.fastq.gz MYB17.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB17.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB18.end1.fastq.gz MYB18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB18.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB19.end1.fastq.gz MYB19.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB19.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB2.end1.fastq.gz MYB2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB20.end1.fastq.gz MYB20.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB20.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB21.end1.fastq.gz MYB21.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB21.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB22.end1.fastq.gz MYB22.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB22.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB23.end1.fastq.gz MYB23.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB23.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB24.end1.fastq.gz MYB24.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB24.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB26.end1.fastq.gz MYB26.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB26.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB27.end1.fastq.gz MYB27.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB27.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB30.end1.fastq.gz MYB30.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB30.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB31.end1.fastq.gz MYB31.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB31.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB32.end1.fastq.gz MYB32.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB32.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB33.end1.fastq.gz MYB33.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB33.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB34.end1.fastq.gz MYB34.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB34.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB36.end1.fastq.gz MYB36.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB36.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py MYB6.end1.fastq.gz MYB6.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - MYB6.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC1.end1.fastq.gz NAC1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC10.end1.fastq.gz NAC10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC10.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC11.end1.fastq.gz NAC11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC11.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC12.end1.fastq.gz NAC12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC12.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC13.end1.fastq.gz NAC13.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC13.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC14.end1.fastq.gz NAC14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC14.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC15.end1.fastq.gz NAC15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC15.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC17.end1.fastq.gz NAC17.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC17.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC18.end1.fastq.gz NAC18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC18.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC2.end1.fastq.gz NAC2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC22.end1.fastq.gz NAC22.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC22.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC23.end1.fastq.gz NAC23.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC23.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC24.end1.fastq.gz NAC24.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC24.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC26.end1.fastq.gz NAC26.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC26.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC27.end1.fastq.gz NAC27.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC27.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC29.end1.fastq.gz NAC29.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC29.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC4.end1.fastq.gz NAC4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC4.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC8.end1.fastq.gz NAC8.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC8.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NAC9.end1.fastq.gz NAC9.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NAC9.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py NF-YC-1.end1.fastq.gz NF-YC-1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - NF-YC-1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SBP3.end1.fastq.gz SBP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SBP3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Trihelix1.end1.fastq.gz Trihelix1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Trihelix1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY10.end1.fastq.gz WRKY10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY10.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY11.end1.fastq.gz WRKY11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY11.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY12.end1.fastq.gz WRKY12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY12.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY13.end1.fastq.gz WRKY13.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY13.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY14.end1.fastq.gz WRKY14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY14.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY15.end1.fastq.gz WRKY15.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY15.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY16.end1.fastq.gz WRKY16.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY16.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY18.end1.fastq.gz WRKY18.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY18.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY19.end1.fastq.gz WRKY19.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY19.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY20.end1.fastq.gz WRKY20.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY20.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY21.end1.fastq.gz WRKY21.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY21.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY30.end1.fastq.gz WRKY30.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY30.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY5.end1.fastq.gz WRKY5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py WRKY8.end1.fastq.gz WRKY8.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - WRKY8.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ZFHD1.end1.fastq.gz ZFHD1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ZFHD1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py ZFHD2.end1.fastq.gz ZFHD2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ZFHD2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH10.end1.fastq.gz bHLH10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH10.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH11.end1.fastq.gz bHLH11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH11.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH12.end1.fastq.gz bHLH12.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH12.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH13.end1.fastq.gz bHLH13.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH13.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH14.end1.fastq.gz bHLH14.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH14.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH16.end1.fastq.gz bHLH16.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH16.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH2.end1.fastq.gz bHLH2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH5.end1.fastq.gz bHLH5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bHLH7.end1.fastq.gz bHLH7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bHLH7.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP1.end1.fastq.gz bZIP1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP1.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP10.end1.fastq.gz bZIP10.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP10.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP11.end1.fastq.gz bZIP11.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP11.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP17.end1.fastq.gz bZIP17.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP17.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP2.end1.fastq.gz bZIP2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP2.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP20.end1.fastq.gz bZIP20.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP20.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP3.end1.fastq.gz bZIP3.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP3.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP4.end1.fastq.gz bZIP4.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP4.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP5.end1.fastq.gz bZIP5.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP5.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP7.end1.fastq.gz bZIP7.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP7.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py bZIP8.end1.fastq.gz bZIP8.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_urartu-Tu2.1/bowtie-indexes/Triticum_urartu-Tu2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - bZIP8.PE.a