python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-14.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - AP2-14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-15.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - AP2-15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-18.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-19.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-19.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-21.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-21.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-7.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-8.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-8.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-DREB-9.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-9.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-ERF-13.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-13.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-ERF-23.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-23.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AP2-RAV-26.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-26.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py B3-10.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - B3-10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2C2-1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2C2-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2C2-2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2C2-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2C2-3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2C2-3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2C2-4.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2C2-4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2C2-5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2C2-5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C2H2-4.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - C2H2-4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C3H-1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C3H-2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py C3H-5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GARP-G2-1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-G2-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GARP2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - GARP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GARP5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - GARP5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GARP6.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - GARP6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py GRAS2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - GRAS2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB-HD-ZIP-2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB-HD-ZIP-3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HB-HD-ZIP-6.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py HSF1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - HSF1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Halo_rep1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Halo_rep2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Halo_rep3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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_rep3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOB2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - LOB2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOB3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - LOB3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOB5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - LOB5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB11.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB12.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB13.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB13.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB14.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB15.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB16.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB16.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB17.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB18.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB19.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB19.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB20.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB20.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB21.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB21.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB22.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB22.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB23.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB23.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB24.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB24.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB26.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB26.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB27.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB27.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB30.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB30.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB31.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB31.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB32.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB32.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB33.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB33.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB34.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB34.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB36.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB36.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py MYB6.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - MYB6.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC10.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC11.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC12.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC13.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC13.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC14.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC15.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC17.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC18.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC22.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC22.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC23.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC23.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC24.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC24.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC26.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC26.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC27.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC27.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC29.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC29.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC4.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC8.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC8.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NAC9.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - NAC9.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py NF-YC-1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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-1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SBP3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - SBP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Trihelix1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - Trihelix1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY10.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY11.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY12.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY13.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY13.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY14.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY15.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY15.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY16.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY16.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY18.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY18.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY19.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY19.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY20.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY20.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY21.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY21.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY30.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY30.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py WRKY8.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - WRKY8.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZFHD1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - ZFHD1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ZFHD2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - ZFHD2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH10.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH11.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH12.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH12.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH13.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH13.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH14.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH14.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH16.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH16.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bHLH7.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bHLH7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP1.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP10.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP10.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP11.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP11.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP17.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP17.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP2.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP20.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP20.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP3.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP4.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP4.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP5.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP5.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP7.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP7.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py bZIP8.end1.fastq.gz 36 -stdout | /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 2 -k 2 -m 1 -t --best --strata -q --sam - | /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 - bZIP8.1x36mers.unique