python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL1G11460.t1_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G11460.t1_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL1G23550.t1_F_vesca_Hawaii-4-F7_DAPi712B03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G23550.t1_F_vesca_Hawaii-4-F7_DAPi712B03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL1G53260.t1_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL1G53260.t1_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL2G28980.t1_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G28980.t1_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL2G32420.t2_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G32420.t2_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL2G40550.t1_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL2G40550.t1_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL3G23910.t2_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL3G23910.t2_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL4G38490.t1_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G38490.t1_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL4G45550.t1_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL4G45550.t1_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL8G10650.t1_F_vesca_Hawaii-4-F7_DAPi712D09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G10650.t1_F_vesca_Hawaii-4-F7_DAPi712D09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AL8G13510.t2_F_vesca_Hawaii-4-F7_DAPi712B08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AL8G13510.t2_F_vesca_Hawaii-4-F7_DAPi712B08-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G01060_F_vesca_Hawaii-4-F7_DAPi712H05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G01060_F_vesca_Hawaii-4-F7_DAPi712H05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G12260_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G12260_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G13260_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G13260_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G18330_F_vesca_Hawaii-4-F7_DAPi712G01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G18330_F_vesca_Hawaii-4-F7_DAPi712G01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G20910_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20910_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G20980_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G20980_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G27730_F_vesca_Hawaii-4-F7_DAPi712C01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G27730_F_vesca_Hawaii-4-F7_DAPi712C01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G29160_F_vesca_Hawaii-4-F7_DAPi712B04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G29160_F_vesca_Hawaii-4-F7_DAPi712B04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G33240_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G33240_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G46768_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G46768_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G49480_F_vesca_Hawaii-4-F7_DAPi712A04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G49480_F_vesca_Hawaii-4-F7_DAPi712A04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G52880_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G52880_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G69180_F_vesca_Hawaii-4-F7_DAPi712G05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69180_F_vesca_Hawaii-4-F7_DAPi712G05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G69690_F_vesca_Hawaii-4-F7_DAPi712C02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69690_F_vesca_Hawaii-4-F7_DAPi712C02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G69780_F_vesca_Hawaii-4-F7_DAPi712A03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G69780_F_vesca_Hawaii-4-F7_DAPi712A03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G72740_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G72740_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G74480_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G74480_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G76420_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76420_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G76880_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G76880_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G79580_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G79580_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT1G80840_F_vesca_Hawaii-4-F7_DAPi712G03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT1G80840_F_vesca_Hawaii-4-F7_DAPi712G03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G01060_F_vesca_Hawaii-4-F7_DAPi712F05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01060_F_vesca_Hawaii-4-F7_DAPi712F05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G01930_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01930_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G01940_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G01940_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G02820_F_vesca_Hawaii-4-F7_DAPi712F08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G02820_F_vesca_Hawaii-4-F7_DAPi712F08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G18550_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G18550_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G22430_F_vesca_Hawaii-4-F7_DAPi712H02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G22430_F_vesca_Hawaii-4-F7_DAPi712H02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G30250_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G30250_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G40620_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G40620_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G45420_F_vesca_Hawaii-4-F7_DAPi712F06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45420_F_vesca_Hawaii-4-F7_DAPi712F06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G45480_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G45480_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G46270_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G46270_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT2G47070_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT2G47070_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G02940_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G02940_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G08500_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G08500_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G12250_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G12250_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G18990_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G18990_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G27010_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G27010_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G50060_F_vesca_Hawaii-4-F7_DAPi712G02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50060_F_vesca_Hawaii-4-F7_DAPi712G02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G50260_F_vesca_Hawaii-4-F7_DAPi712D02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50260_F_vesca_Hawaii-4-F7_DAPi712D02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G50410_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G50410_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G56400_F_vesca_Hawaii-4-F7_DAPi712B02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G56400_F_vesca_Hawaii-4-F7_DAPi712B02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G57920_F_vesca_Hawaii-4-F7_DAPi712D06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G57920_F_vesca_Hawaii-4-F7_DAPi712D06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT3G60530_F_vesca_Hawaii-4-F7_DAPi712E05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT3G60530_F_vesca_Hawaii-4-F7_DAPi712E05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G00730_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G00730_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G14770_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G14770_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G17980_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G17980_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G25470_F_vesca_Hawaii-4-F7_DAPi712B06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25470_F_vesca_Hawaii-4-F7_DAPi712B06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G25480_F_vesca_Hawaii-4-F7_DAPi712F04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25480_F_vesca_Hawaii-4-F7_DAPi712F04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G25490_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G25490_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT4G31800_F_vesca_Hawaii-4-F7_DAPi712F02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT4G31800_F_vesca_Hawaii-4-F7_DAPi712F02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G02320_F_vesca_Hawaii-4-F7_DAPi712G06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G02320_F_vesca_Hawaii-4-F7_DAPi712G06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G03150_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03150_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G03790_F_vesca_Hawaii-4-F7_DAPi712C06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G03790_F_vesca_Hawaii-4-F7_DAPi712C06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G05550_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G05550_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G09410_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G09410_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G10030_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G10030_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G11260_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G11260_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G14960_F_vesca_Hawaii-4-F7_DAPi712E08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G14960_F_vesca_Hawaii-4-F7_DAPi712E08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G17300_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G17300_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G18560_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G18560_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G19790_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G19790_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G39760_F_vesca_Hawaii-4-F7_DAPi712A02-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G39760_F_vesca_Hawaii-4-F7_DAPi712A02-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G45300_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G45300_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G47390_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G47390_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G52830_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G52830_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G56110_F_vesca_Hawaii-4-F7_DAPi712E06-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G56110_F_vesca_Hawaii-4-F7_DAPi712E06-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G60130_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G60130_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G62020_F_vesca_Hawaii-4-F7_DAPi712E04-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62020_F_vesca_Hawaii-4-F7_DAPi712E04-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G62470_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62470_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G62940_F_vesca_Hawaii-4-F7_DAPi712A05-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G62940_F_vesca_Hawaii-4-F7_DAPi712A05-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G64750_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G64750_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G65410_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G65410_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py AT5G67300_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AT5G67300_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0001s0116.1_F_vesca_Hawaii-4-F7_DAPi712C10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s0116.1_F_vesca_Hawaii-4-F7_DAPi712C10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0001s1194.1_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s1194.1_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0001s3581.1.p_F_vesca_Hawaii-4-F7_DAPi712D01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0001s3581.1.p_F_vesca_Hawaii-4-F7_DAPi712D01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0002s1646.1_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1646.1_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0002s1959.1_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s1959.1_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0002s2670.1_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0002s2670.1_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0003s1161.1.p_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0003s1161.1.p_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0004s2291.1_F_vesca_Hawaii-4-F7_DAPi712A09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2291.1_F_vesca_Hawaii-4-F7_DAPi712A09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0004s2898.1.p_F_vesca_Hawaii-4-F7_DAPi712B07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0004s2898.1.p_F_vesca_Hawaii-4-F7_DAPi712B07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0008s0039.1_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0039.1_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Carub.0008s0285.1_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Carub.0008s0285.1_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P220.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P220.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os01g17260.2_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g17260.2_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os01g18240.1_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g18240.1_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os01g46970.1_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g46970.1_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os01g51154.1_F_vesca_Hawaii-4-F7_DAPi712A11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os01g51154.1_F_vesca_Hawaii-4-F7_DAPi712A11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os02g33430.1_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g33430.1_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os02g42970.1_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os02g42970.1_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os03g21800.1_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os03g21800.1_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os06g07030.1_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os06g07030.1_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os08g06110.3_F_vesca_Hawaii-4-F7_DAPi712D10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g06110.3_F_vesca_Hawaii-4-F7_DAPi712D10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os08g37970.1_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os08g37970.1_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os09g25060.1_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os09g25060.1_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os10g26500.1_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g26500.1_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py LOC_Os10g41200.1_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - LOC_Os10g41200.1_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc01g095460.3.1_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g095460.3.1_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc01g102340.3.1_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc01g102340.3.1_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc03g116890.3.1_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc03g116890.3.1_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc04g078640.3.1_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc04g078640.3.1_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc05g007180.3.1_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc05g007180.3.1_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc06g048630.3.1_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc06g048630.3.1_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc07g040920.2.1_F_vesca_Hawaii-4-F7_DAPi712B11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc07g040920.2.1_F_vesca_Hawaii-4-F7_DAPi712B11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc08g068320.3.1_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g068320.3.1_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc08g078340.3.1_F_vesca_Hawaii-4-F7_DAPi712H09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g078340.3.1_F_vesca_Hawaii-4-F7_DAPi712H09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc08g079120.3.1_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc08g079120.3.1_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc10g005080.3.1_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc10g005080.3.1_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py Solyc11g064950.3.1_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Solyc11g064950.3.1_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013586407.1_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013586407.1_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013587350.1_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587350.1_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013587997.1_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013587997.1_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013589913.1_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589913.1_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013589953.1_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013589953.1_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013602769.1_F_vesca_Hawaii-4-F7_DAPi712C03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013602769.1_F_vesca_Hawaii-4-F7_DAPi712C03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013609718.1_F_vesca_Hawaii-4-F7_DAPi712G12-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013609718.1_F_vesca_Hawaii-4-F7_DAPi712G12-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013613838.1_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013613838.1_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013615900.1_F_vesca_Hawaii-4-F7_DAPi712E09-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013615900.1_F_vesca_Hawaii-4-F7_DAPi712E09-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013629448.1_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013629448.1_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013631386.1_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631386.1_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013631649.1_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013631649.1_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P247.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py XP_013634112.1_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P247.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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic -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/Fragaria_vesca_subsp._vesca-FraVesHawaii_1.0/bowtie-indexes/GCA_000184155.1_FraVesHawaii_1.0_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - XP_013634112.1_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P247.1x36mers.unique