python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L01_exp230404_MS06_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L02_exp230404_MS74_SCD-MET_20min-DMSO_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L03_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L04_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L05_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-A.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L06_exp230404_MS06_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L07_exp230404_MS74_SCD-MET_20min-DMSO_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L08_exp230404_MS74_SCD-MET_20min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L09_exp230404_MS74_SCD-MET_40min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.end1.fastq.gz 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.230604_NB551514_0060_AHCTG5BGXT.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 - 2023-05-22-MS230430L10_exp230404_MS74_SCD-MET_60min-10nM-PhIAA_DNA-B.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a