python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2832-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_1___2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2832-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_1___2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2832-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_1___2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2833-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_2___2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2833-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_2___2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2833-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_2___2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2834-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_3___2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2834-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_3___2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2834-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_100_3___2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2835-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_1___2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2835-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_1___2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2835-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_1___2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2836-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_2___2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2836-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_2___2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2836-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_2___2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2837-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_3___2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2837-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_3___2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2837-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_10_3___2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2838-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_1____2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2838-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_1____2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2838-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_1____2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L2839-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_2____2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L2839-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_2____2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz L2839-Bdellovibrio_bacteriovorus_ICPB_3264_HEPES_1_2____2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.end1.fastq.gz 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.230617_NB551514_0063_AHGVMKBGXT.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 - 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a