python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L01_exp201101_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L01_exp201101_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L01_exp201101_MS625_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L01_exp201101_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L01_exp201101_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L02_exp201101_MS626_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L02_exp201101_MS626_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L02_exp201101_MS626_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L02_exp201101_MS626_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L02_exp201101_MS626_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L03_exp201101_MS628_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L03_exp201101_MS628_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L03_exp201101_MS628_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L03_exp201101_MS628_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L03_exp201101_MS628_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L04_exp201101_MS629_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L04_exp201101_MS629_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L04_exp201101_MS629_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L04_exp201101_MS629_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L04_exp201101_MS629_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L05_exp201101_MS630_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L05_exp201101_MS630_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L05_exp201101_MS630_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L05_exp201101_MS630_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L05_exp201101_MS630_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L06_exp201101_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L06_exp201101_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L06_exp201101_MS205_SCD_RAPA-65min_input.end1.fastq.gz 2020-12-17-201116L06_exp201101_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L06_exp201101_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L07_exp201102A_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L07_exp201102A_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L07_exp201102A_MS625_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L07_exp201102A_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L07_exp201102A_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L08_exp201102A_MS631_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L08_exp201102A_MS631_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L08_exp201102A_MS631_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L08_exp201102A_MS631_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L08_exp201102A_MS631_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L09_exp201102A_MS632_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L09_exp201102A_MS632_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L09_exp201102A_MS632_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L09_exp201102A_MS632_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L09_exp201102A_MS632_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L10_exp201102A_MS633_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L10_exp201102A_MS633_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L10_exp201102A_MS633_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L10_exp201102A_MS633_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L10_exp201102A_MS633_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L11_exp201102A_MS636_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L11_exp201102A_MS636_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L11_exp201102A_MS636_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L11_exp201102A_MS636_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L11_exp201102A_MS636_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L12_exp201102A_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L12_exp201102A_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L12_exp201102A_MS205_SCD_RAPA-65min_input.end1.fastq.gz 2020-12-17-201116L12_exp201102A_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L12_exp201102A_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L13_exp201102B_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L13_exp201102B_MS625_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L13_exp201102B_MS625_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L13_exp201102B_MS625_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L13_exp201102B_MS625_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L14_exp201102B_MS634_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L14_exp201102B_MS634_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L14_exp201102B_MS634_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L14_exp201102B_MS634_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L14_exp201102B_MS634_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L15_exp201102B_MS635_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L15_exp201102B_MS635_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L15_exp201102B_MS635_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L15_exp201102B_MS635_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L15_exp201102B_MS635_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L16_exp201102B_MS638_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L16_exp201102B_MS638_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L16_exp201102B_MS638_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L16_exp201102B_MS638_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L16_exp201102B_MS638_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L17_exp201102B_MS641_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L17_exp201102B_MS641_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L17_exp201102B_MS641_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L17_exp201102B_MS641_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L17_exp201102B_MS641_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L18_exp201102B_MS648_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L18_exp201102B_MS648_SCD_ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L18_exp201102B_MS648_SCD_ATC-45min_input.end1.fastq.gz 2020-12-17-201116L18_exp201102B_MS648_SCD_ATC-45min_input.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 -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 - 2020-12-17-201116L18_exp201102B_MS648_SCD_ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L19_exp201102B_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L19_exp201102B_MS205_SCD_RAPA-65min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L19_exp201102B_MS205_SCD_RAPA-65min_input.end1.fastq.gz 2020-12-17-201116L19_exp201102B_MS205_SCD_RAPA-65min_input.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 -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 - 2020-12-17-201116L19_exp201102B_MS205_SCD_RAPA-65min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L20_exp201101_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L20_exp201101_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L20_exp201101_MS625_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L20_exp201101_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L20_exp201101_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L21_exp201101_MS626_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L21_exp201101_MS626_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L21_exp201101_MS626_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L21_exp201101_MS626_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L21_exp201101_MS626_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L22_exp201101_MS628_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L22_exp201101_MS628_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L22_exp201101_MS628_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L22_exp201101_MS628_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L22_exp201101_MS628_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L23_exp201101_MS629_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L23_exp201101_MS629_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L23_exp201101_MS629_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L23_exp201101_MS629_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L23_exp201101_MS629_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L24_exp201101_MS630_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L24_exp201101_MS630_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L24_exp201101_MS630_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L24_exp201101_MS630_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L24_exp201101_MS630_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.end1.fastq.gz 2020-12-17-201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L25_exp201101_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L26_exp201102A_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L26_exp201102A_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L26_exp201102A_MS625_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L26_exp201102A_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L26_exp201102A_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L27_exp201102A_MS631_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L27_exp201102A_MS631_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L27_exp201102A_MS631_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L27_exp201102A_MS631_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L27_exp201102A_MS631_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L28_exp201102A_MS632_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L28_exp201102A_MS632_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L28_exp201102A_MS632_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L28_exp201102A_MS632_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L28_exp201102A_MS632_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L29_exp201102A_MS633_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L29_exp201102A_MS633_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L29_exp201102A_MS633_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L29_exp201102A_MS633_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L29_exp201102A_MS633_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L30_exp201102A_MS636_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L30_exp201102A_MS636_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L30_exp201102A_MS636_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L30_exp201102A_MS636_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L30_exp201102A_MS636_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L31_exp201102A_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L31_exp201102A_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L31_exp201102A_MS205_SCD_RAPA-65min_AB01.end1.fastq.gz 2020-12-17-201116L31_exp201102A_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L31_exp201102A_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L32_exp201102B_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L32_exp201102B_MS625_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L32_exp201102B_MS625_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L32_exp201102B_MS625_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L32_exp201102B_MS625_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L33_exp201102B_MS634_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L33_exp201102B_MS634_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L33_exp201102B_MS634_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L33_exp201102B_MS634_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L33_exp201102B_MS634_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L34_exp201102B_MS635_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L34_exp201102B_MS635_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L34_exp201102B_MS635_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L34_exp201102B_MS635_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L34_exp201102B_MS635_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L35_exp201102B_MS638_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L35_exp201102B_MS638_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L35_exp201102B_MS638_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L35_exp201102B_MS638_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L35_exp201102B_MS638_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L36_exp201102B_MS641_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L36_exp201102B_MS641_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L36_exp201102B_MS641_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L36_exp201102B_MS641_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L36_exp201102B_MS641_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L37_exp201102B_MS648_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L37_exp201102B_MS648_SCD_ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L37_exp201102B_MS648_SCD_ATC-45min_AB01.end1.fastq.gz 2020-12-17-201116L37_exp201102B_MS648_SCD_ATC-45min_AB01.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 -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 - 2020-12-17-201116L37_exp201102B_MS648_SCD_ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201116L38_exp201102B_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L38_exp201102B_MS205_SCD_RAPA-65min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201116L38_exp201102B_MS205_SCD_RAPA-65min_AB01.end1.fastq.gz 2020-12-17-201116L38_exp201102B_MS205_SCD_RAPA-65min_AB01.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 -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 - 2020-12-17-201116L38_exp201102B_MS205_SCD_RAPA-65min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L01_exp2011_MK918_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L01_exp2011_MK918_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L01_exp2011_MK918_SCD_DMSO_AB107.end1.fastq.gz 2020-12-17-201119L01_exp2011_MK918_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L01_exp2011_MK918_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L02_exp2011_MK918_SCD_1NMPP1-01min_AB107.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 -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 - 2020-12-17-201119L02_exp2011_MK918_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L02_exp2011_MK918_SCD_1NMPP1-01min_AB107.end1.fastq.gz 2020-12-17-201119L02_exp2011_MK918_SCD_1NMPP1-01min_AB107.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 -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 - 2020-12-17-201119L02_exp2011_MK918_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L03_exp2011_MK918_SCD_1NMPP1-03min_AB107.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 -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 - 2020-12-17-201119L03_exp2011_MK918_SCD_1NMPP1-03min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L03_exp2011_MK918_SCD_1NMPP1-03min_AB107.end1.fastq.gz 2020-12-17-201119L03_exp2011_MK918_SCD_1NMPP1-03min_AB107.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 -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 - 2020-12-17-201119L03_exp2011_MK918_SCD_1NMPP1-03min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L04_exp2011_MK918_SCD_1NMPP1-10min_AB107.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 -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 - 2020-12-17-201119L04_exp2011_MK918_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L04_exp2011_MK918_SCD_1NMPP1-10min_AB107.end1.fastq.gz 2020-12-17-201119L04_exp2011_MK918_SCD_1NMPP1-10min_AB107.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 -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 - 2020-12-17-201119L04_exp2011_MK918_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L05_exp2011_MK978_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L05_exp2011_MK978_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L05_exp2011_MK978_SCD_DMSO_AB107.end1.fastq.gz 2020-12-17-201119L05_exp2011_MK978_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L05_exp2011_MK978_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L06_exp2011_MK978_SCD_1NMPP1-01min_AB107.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 -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 - 2020-12-17-201119L06_exp2011_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L06_exp2011_MK978_SCD_1NMPP1-01min_AB107.end1.fastq.gz 2020-12-17-201119L06_exp2011_MK978_SCD_1NMPP1-01min_AB107.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 -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 - 2020-12-17-201119L06_exp2011_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L07_exp2011_MK978_SCD_1NMPP1-10min_AB107.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 -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 - 2020-12-17-201119L07_exp2011_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L07_exp2011_MK978_SCD_1NMPP1-10min_AB107.end1.fastq.gz 2020-12-17-201119L07_exp2011_MK978_SCD_1NMPP1-10min_AB107.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 -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 - 2020-12-17-201119L07_exp2011_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L08_exp2011_MK846_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L08_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L08_exp2011_MK846_SCD_DMSO_AB107.end1.fastq.gz 2020-12-17-201119L08_exp2011_MK846_SCD_DMSO_AB107.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 -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 - 2020-12-17-201119L08_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L09_exp2011_MK846_SCD_RAPA-30min_AB107.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 -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 - 2020-12-17-201119L09_exp2011_MK846_SCD_RAPA-30min_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L09_exp2011_MK846_SCD_RAPA-30min_AB107.end1.fastq.gz 2020-12-17-201119L09_exp2011_MK846_SCD_RAPA-30min_AB107.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 -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 - 2020-12-17-201119L09_exp2011_MK846_SCD_RAPA-30min_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L10_exp200916_MK918_SCD_DMSO_AB03.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 -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 - 2020-12-17-201119L10_exp200916_MK918_SCD_DMSO_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L10_exp200916_MK918_SCD_DMSO_AB03.end1.fastq.gz 2020-12-17-201119L10_exp200916_MK918_SCD_DMSO_AB03.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 -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 - 2020-12-17-201119L10_exp200916_MK918_SCD_DMSO_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.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 -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 - 2020-12-17-201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.end1.fastq.gz 2020-12-17-201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.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 -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 - 2020-12-17-201119L11_exp200916_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.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 -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 - 2020-12-17-201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.end1.fastq.gz 2020-12-17-201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.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 -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 - 2020-12-17-201119L12_exp200916_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L13_exp200916_MK918_SCD_1NMPP1-1min_AB03.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 -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 - 2020-12-17-201119L13_exp200916_MK918_SCD_1NMPP1-1min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L13_exp200916_MK918_SCD_1NMPP1-1min_AB03.end1.fastq.gz 2020-12-17-201119L13_exp200916_MK918_SCD_1NMPP1-1min_AB03.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 -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 - 2020-12-17-201119L13_exp200916_MK918_SCD_1NMPP1-1min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L14_exp2011_MK918_SCD_DMSO_AB03.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 -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 - 2020-12-17-201119L14_exp2011_MK918_SCD_DMSO_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L14_exp2011_MK918_SCD_DMSO_AB03.end1.fastq.gz 2020-12-17-201119L14_exp2011_MK918_SCD_DMSO_AB03.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 -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 - 2020-12-17-201119L14_exp2011_MK918_SCD_DMSO_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L15_exp2011_MK918_SCD_1NMPP1-01min_AB03.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 -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 - 2020-12-17-201119L15_exp2011_MK918_SCD_1NMPP1-01min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L15_exp2011_MK918_SCD_1NMPP1-01min_AB03.end1.fastq.gz 2020-12-17-201119L15_exp2011_MK918_SCD_1NMPP1-01min_AB03.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 -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 - 2020-12-17-201119L15_exp2011_MK918_SCD_1NMPP1-01min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L16_exp2011_MK918_SCD_1NMPP1-03min_AB03.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 -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 - 2020-12-17-201119L16_exp2011_MK918_SCD_1NMPP1-03min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L16_exp2011_MK918_SCD_1NMPP1-03min_AB03.end1.fastq.gz 2020-12-17-201119L16_exp2011_MK918_SCD_1NMPP1-03min_AB03.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 -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 - 2020-12-17-201119L16_exp2011_MK918_SCD_1NMPP1-03min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L17_exp2011_MK918_SCD_1NMPP1-1min_AB03.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 -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 - 2020-12-17-201119L17_exp2011_MK918_SCD_1NMPP1-1min_AB03.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L17_exp2011_MK918_SCD_1NMPP1-1min_AB03.end1.fastq.gz 2020-12-17-201119L17_exp2011_MK918_SCD_1NMPP1-1min_AB03.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 -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 - 2020-12-17-201119L17_exp2011_MK918_SCD_1NMPP1-1min_AB03.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L18_exp2011_MK679_SCGE_AB101.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 -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 - 2020-12-17-201119L18_exp2011_MK679_SCGE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L18_exp2011_MK679_SCGE_AB101.end1.fastq.gz 2020-12-17-201119L18_exp2011_MK679_SCGE_AB101.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 -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 - 2020-12-17-201119L18_exp2011_MK679_SCGE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2020-12-17-201119L19_exp2011_MK711_SCGE_AB101.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 -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 - 2020-12-17-201119L19_exp2011_MK711_SCGE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2020-12-17-201119L19_exp2011_MK711_SCGE_AB101.end1.fastq.gz 2020-12-17-201119L19_exp2011_MK711_SCGE_AB101.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 -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 - 2020-12-17-201119L19_exp2011_MK711_SCGE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a