python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP1.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP1.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP2.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP2.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP3.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py ChCUC1_halo_REP3.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ChCUC1_halo_REP3.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP1.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP1.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP1.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP1.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP2.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP2.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP2.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP2.SE.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP3.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP3.1x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py halo_REP3.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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1 -p 20 -v 1 -a -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/Cardamine_hirsuta-ddCarHirs1.hap2.1/bowtie-indexes/Cardamine_hirsuta-ddCarHirs1.hap2.1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - halo_REP3.SE.a