python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL11A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL11A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL11B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL11B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL12B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL12B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL13A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL13A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL13B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL13B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL13D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL13D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL14B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL14B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL15A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL15A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL15B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL15B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL15D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL15D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL16A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL16A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL16D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL16D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL18A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL18A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL18D2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL18D2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL19B_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL19B_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL19B_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL19B_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL1D_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL1D_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL1D_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL1D_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL2A_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL2A_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL2A_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL2A_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL2B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL2B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL2D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL2D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL3A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL3A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL3B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL3B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL3D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL3D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL4A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL4A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL4B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL4B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL4D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL4D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL5A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL5A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL5B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL5B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL5D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL5D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL6A_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL6A_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL6A_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL6A_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL6B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL6B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL6D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL6D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL7A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL7A.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL7B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL7B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL7D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL7D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL8A_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL8A_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL8A_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL8A_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL8B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL8B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL8D1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL8D1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL9A_rep1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL9A_rep1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL9A_rep2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL9A_rep2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL9B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL9B.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py SPL9D.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - SPL9D.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Ta-input.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ta-input.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Ta-input2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Ta-input2.1x36mers.unique