python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL11A.end1.fastq.gz SPL11A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL11B.end1.fastq.gz SPL11B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL12B.end1.fastq.gz SPL12B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL13A.end1.fastq.gz SPL13A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL13B.end1.fastq.gz SPL13B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL13D.end1.fastq.gz SPL13D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL14B.end1.fastq.gz SPL14B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL15A.end1.fastq.gz SPL15A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL15B.end1.fastq.gz SPL15B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL15D.end1.fastq.gz SPL15D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL16A.end1.fastq.gz SPL16A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL16D.end1.fastq.gz SPL16D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL18A.end1.fastq.gz SPL18A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL18D2.end1.fastq.gz SPL18D2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL19B_rep1.end1.fastq.gz SPL19B_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL19B_rep2.end1.fastq.gz SPL19B_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL1D_rep1.end1.fastq.gz SPL1D_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL1D_rep2.end1.fastq.gz SPL1D_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL2A_rep1.end1.fastq.gz SPL2A_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL2A_rep2.end1.fastq.gz SPL2A_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL2B.end1.fastq.gz SPL2B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL2D.end1.fastq.gz SPL2D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL3A.end1.fastq.gz SPL3A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL3B.end1.fastq.gz SPL3B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL3D.end1.fastq.gz SPL3D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL4A.end1.fastq.gz SPL4A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL4B.end1.fastq.gz SPL4B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL4D.end1.fastq.gz SPL4D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL5A.end1.fastq.gz SPL5A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL5B.end1.fastq.gz SPL5B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL5D.end1.fastq.gz SPL5D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL6A_rep1.end1.fastq.gz SPL6A_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL6A_rep2.end1.fastq.gz SPL6A_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL6B.end1.fastq.gz SPL6B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL6D.end1.fastq.gz SPL6D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL7A.end1.fastq.gz SPL7A.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL7B.end1.fastq.gz SPL7B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL7D.end1.fastq.gz SPL7D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL8A_rep1.end1.fastq.gz SPL8A_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL8A_rep2.end1.fastq.gz SPL8A_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL8B.end1.fastq.gz SPL8B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL8D1.end1.fastq.gz SPL8D1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL9A_rep1.end1.fastq.gz SPL9A_rep1.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL9A_rep2.end1.fastq.gz SPL9A_rep2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL9B.end1.fastq.gz SPL9B.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py SPL9D.end1.fastq.gz SPL9D.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Ta-input.end1.fastq.gz Ta-input.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Ta-input2.end1.fastq.gz Ta-input2.end2.fastq.gz -trim 75 75 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/bowtie-indexes/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1 -p 20 -v 1 -a -t --best --strata -q -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_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.PE.a