python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L01_exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L02_exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L03_exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L04_exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1/2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L05_exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1/2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L06_exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1/2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L07_exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1/2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240628L08_exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L09_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L10_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L11_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L12_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B/2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L13_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L14_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B/2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L15_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B/2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240712L16_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L01_exp240521_MS857_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L02_exp240521_MS857_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L03_exp240521_MS857_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L04_exp240521_MS857_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A/2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L05_exp240521_MS857_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L06_exp240521_MS857_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A/2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L07_exp240521_MS857_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A/2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240718L08_exp240521_MS857_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L13_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L14_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L15_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L16_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L17_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L18_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L19_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L20_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L21_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A/2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L22_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A/2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L23_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A/2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L24_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-A.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L37_exp240718_MS798_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L38_exp240718_MS798_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L39_exp240718_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L40_exp240718_MS798_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L41_exp240718_MS798_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L42_exp240718_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L43_exp240514_MS498_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L44_exp240514_MS498_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L45_exp240514_MS498_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L46_exp240514_MS498_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L47_exp240514_MS498_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240731L48_exp240514_MS498_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L01_exp240514_MS69_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L02_exp240514_MS69_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L03_exp240514_MS69_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L04_exp240514_MS69_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L05_exp240514_MS69_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L06_exp240514_MS69_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L07_exp240718_MS799_SCGE_1.5hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L08_exp240718_MS799_SCGE_1.5hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L09_exp240718_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B/2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L10_exp240718_MS799_SCGE_8hr-arrest_1hr-DMSO_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B/2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L11_exp240718_MS799_SCGE_8hr-arrest_1hr-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B/2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L12_exp240718_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-B.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L13_exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L14_exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L15_exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L16_exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L17_exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L18_exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L19_exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L20_exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L21_exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2/2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L22_exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2/2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L23_exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -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/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-gDNA/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2/2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-09-13-MS240813L24_exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a