python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1-MS240604L34-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1-MS240604L34.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1-MS240604L34-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1-MS240604L34-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-1-MS240604L34.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-2-MS240614L34R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-2-MS240614L34R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-2-MS240614L34R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-2-MS240614L34R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-2-MS240614L34R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-3-MS240617L02-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-3-MS240617L02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-3-MS240617L02-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-3-MS240617L02-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-DMSO_gDNA-3-MS240617L02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L33-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L33.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L33-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L33-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L33.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L33R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L33R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L33R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L33R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L33R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L01-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L01-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L01-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_2hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1-MS240604L36-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1-MS240604L36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1-MS240604L36-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1-MS240604L36-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-1-MS240604L36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-2-MS240614L36R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-2-MS240614L36R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-2-MS240614L36R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-2-MS240614L36R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-2-MS240614L36R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-3-MS240617L04-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-3-MS240617L04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-3-MS240617L04-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-3-MS240617L04-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-DMSO_gDNA-3-MS240617L04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L35-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L35.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L35-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L35-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L35.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L35R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L35R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L35R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L35R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L35R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L03-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L03-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L03-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1-MS240604L39-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1-MS240604L39.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1-MS240604L39-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1-MS240604L39-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-1-MS240604L39.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-2-MS240614L39R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-2-MS240614L39R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-2-MS240614L39R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-2-MS240614L39R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-2-MS240614L39R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-3-MS240617L07-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-3-MS240617L07.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-3-MS240617L07-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-3-MS240617L07-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_5hr-arrest_4hr-Rapamycin_gDNA-3-MS240617L07.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1-MS240604L38-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1-MS240604L38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1-MS240604L38-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1-MS240604L38-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-1-MS240604L38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-2-MS240614L38R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-2-MS240614L38R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-2-MS240614L38R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-2-MS240614L38R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-2-MS240614L38R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-3-MS240617L06-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-3-MS240617L06.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-3-MS240617L06-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-3-MS240617L06-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-DMSO_gDNA-3-MS240617L06.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L37-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L37-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L37-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-1-MS240604L37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L37R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L37R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L37R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L37R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-2-MS240614L37R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L05-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L05-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L05-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_1hr-Rapamycin_gDNA-3-MS240617L05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1-MS240604L40-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1-MS240604L40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1-MS240604L40-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1-MS240604L40-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-1-MS240604L40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-2-MS240614L40R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-2-MS240614L40R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-2-MS240614L40R-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-2-MS240614L40R-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-2-MS240614L40R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-3-MS240617L08-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-3-MS240617L08.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-3-MS240617L08-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-3-MS240617L08-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240502_MS412_SCD-Met_8hr-arrest_7hr-Rapamycin_gDNA-3-MS240617L08.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L23-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L23.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L23-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L23-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L23.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L21-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L21-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L21-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L22-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L22.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L22-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L22-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L22.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L26-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L26.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L26-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L26-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L26.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L24-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L24.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L24-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L24-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L24.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L25-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L25.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L25-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L25-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240514_MS497_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L25.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L29-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L29.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L29-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L29-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240604L29.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L27-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L27.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L27-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L27-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240604L27.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L28-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L28.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L28-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L28-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240604L28.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L32-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L32.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L32-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L32-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240604L32.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L30-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L30.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L30-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L30-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240604L30.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L31-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L31.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L31-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L31-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240517_MS798_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240604L31.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L03-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L03-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L03-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L01-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L01-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L01-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L02-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L02-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L02-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L06-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L06.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L06-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L06-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L06.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L04-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L04-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L04-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L05-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L05-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L05-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS799_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L09-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L09.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L09-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L09-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_30min-PhIAA_gDNA-MS240618L09.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L07-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L07.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L07-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L07-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-DMSO_gDNA-MS240618L07.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L08-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L08.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L08-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L08-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_1.5hr-arrest_60min-PhIAA_gDNA-MS240618L08.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L12-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L12.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L12-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L12-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_30min-PhIAA_gDNA-MS240618L12.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L10-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L10.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L10-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L10-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-DMSO_gDNA-MS240618L10.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L11-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L11.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L11-EKDL240031697-1A_22CJ5VLT4_L8.end1.fastq.gz 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L11-EKDL240031697-1A_22CJ5VLT4_L8.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+C_glabrata_CBS138_current_chromosomes -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+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2024-07-09-exp240607_MS800_SCGE_8hr-arrest_60min-PhIAA_gDNA-MS240618L11.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a