python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3692-Leptospira_biflexa_serovar_Patoc_KAS_rep1.250319_NB551514_0272_AHKVJYBGYW.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/Bacteria/Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris-ASM1768v1/bowtie-indexes/Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris-ASM1768v1 -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/Bacteria/Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris-ASM1768v1/bowtie-indexes/Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris-ASM1768v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3692-Leptospira_biflexa_serovar_Patoc_KAS_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3694-Leptospira_interrogans_serovar_Manilae_KAS_rep1.250319_NB551514_0272_AHKVJYBGYW.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/Bacteria/Leptospira_interrogans_serovar_Manilae-ASM104763v1/bowtie-indexes/Leptospira_interrogans_serovar_Manilae-ASM104763v1 -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/Bacteria/Leptospira_interrogans_serovar_Manilae-ASM104763v1/bowtie-indexes/Leptospira_interrogans_serovar_Manilae-ASM104763v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3694-Leptospira_interrogans_serovar_Manilae_KAS_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3695-Leptospira_interrogans_serovar_Manilae_KAS_rep2.250319_NB551514_0272_AHKVJYBGYW.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/Bacteria/Leptospira_interrogans_serovar_Manilae-ASM104763v1/bowtie-indexes/Leptospira_interrogans_serovar_Manilae-ASM104763v1 -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/Bacteria/Leptospira_interrogans_serovar_Manilae-ASM104763v1/bowtie-indexes/Leptospira_interrogans_serovar_Manilae-ASM104763v1.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3695-Leptospira_interrogans_serovar_Manilae_KAS_rep2.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3696-K562_KLF1_rep1.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3696-K562_KLF1_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3697-K562_KLF1_rep1.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3697-K562_KLF1_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3702-K562_NRSF_test_CST.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3702-K562_NRSF_test_CST.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3703-K562_NRSF_test_MA5-44189.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3703-K562_NRSF_test_MA5-44189.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3704-K562_NRSF_test_MA5-35361.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3704-K562_NRSF_test_MA5-35361.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3705-K562_NRSF_test_MA5-55715.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3705-K562_NRSF_test_MA5-55715.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3706-K562_NRSF_test-ZR31455-25UL.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3706-K562_NRSF_test-ZR31455-25UL.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3707-ATF4_ATF4pos_rep1.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3707-ATF4_ATF4pos_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3708-ATF4_ATF4pos_rep2.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3708-ATF4_ATF4pos_rep2.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3709-ATF4_GFP_rep1.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3709-ATF4_GFP_rep1.1x50mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L3710-ATF4_GFP_rep2.250319_NB551514_0272_AHKVJYBGYW.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/hg38/bowtie-indexes/hg38-male -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/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L3710-ATF4_GFP_rep2.1x50mers.unique