python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L01_MS1_input/2019-03-13-181105L01_MS1_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D073_181105L01_exp180712_MS01_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L01_MS1_input/2019-03-13-181105L01_MS1_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L01_MS1_input/2019-03-13-181105L01_MS1_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D073_181105L01_exp180712_MS01_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L02_MS80_input/2019-03-13-181105L02_MS80_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D074_181105L02_exp180712_MS80_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L02_MS80_input/2019-03-13-181105L02_MS80_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L02_MS80_input/2019-03-13-181105L02_MS80_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D074_181105L02_exp180712_MS80_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L03_MS81_input/2019-03-13-181105L03_MS81_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D075_181105L03_exp180712_MS81_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L03_MS81_input/2019-03-13-181105L03_MS81_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L03_MS81_input/2019-03-13-181105L03_MS81_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D075_181105L03_exp180712_MS81_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L04_MS63_0nM_input/2019-03-13-181105L04_MS63_0nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D076_181105L04_exp180712_MS63_0nM_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L04_MS63_0nM_input/2019-03-13-181105L04_MS63_0nM_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L04_MS63_0nM_input/2019-03-13-181105L04_MS63_0nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D076_181105L04_exp180712_MS63_0nM_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L05_MS63_10nM_input/2019-03-13-181105L05_MS63_10nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D077_181105L05_exp180712_MS63_10nM_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L05_MS63_10nM_input/2019-03-13-181105L05_MS63_10nM_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L05_MS63_10nM_input/2019-03-13-181105L05_MS63_10nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D077_181105L05_exp180712_MS63_10nM_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L06_MS63_30nM_input/2019-03-13-181105L06_MS63_30nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D078_181105L06_exp180712_MS63_30nM_input_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L06_MS63_30nM_input/2019-03-13-181105L06_MS63_30nM_input.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-181105L06_MS63_30nM_input/2019-03-13-181105L06_MS63_30nM_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 -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D078_181105L06_exp180712_MS63_30nM_input_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L07_MS1_AB20-H3/2019-03-13-190204L07_MS1_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D079_190204L07_exp180712_MS01_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L07_MS1_AB20-H3/2019-03-13-190204L07_MS1_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L07_MS1_AB20-H3/2019-03-13-190204L07_MS1_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D079_190204L07_exp180712_MS01_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L08_MS80_AB20-H3/2019-03-13-190204L08_MS80_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D080_190204L08_exp180712_MS80_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L08_MS80_AB20-H3/2019-03-13-190204L08_MS80_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L08_MS80_AB20-H3/2019-03-13-190204L08_MS80_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D080_190204L08_exp180712_MS80_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L09_MS81_AB20-H3/2019-03-13-190204L09_MS81_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D081_190204L09_exp180712_MS81_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L09_MS81_AB20-H3/2019-03-13-190204L09_MS81_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L09_MS81_AB20-H3/2019-03-13-190204L09_MS81_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D081_190204L09_exp180712_MS81_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L10_MS63_0nM_AB20-H3/2019-03-13-190204L10_MS63_0nM_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D082_190204L10_exp180712_MS63_0nM_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L10_MS63_0nM_AB20-H3/2019-03-13-190204L10_MS63_0nM_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L10_MS63_0nM_AB20-H3/2019-03-13-190204L10_MS63_0nM_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D082_190204L10_exp180712_MS63_0nM_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L11_MS63_10nM_AB20-H3/2019-03-13-190204L11_MS63_10nM_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D083_190204L11_exp180712_MS63_10nM_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L11_MS63_10nM_AB20-H3/2019-03-13-190204L11_MS63_10nM_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L11_MS63_10nM_AB20-H3/2019-03-13-190204L11_MS63_10nM_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D083_190204L11_exp180712_MS63_10nM_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L12_MS63_30nM_AB20-H3/2019-03-13-190204L12_MS63_30nM_AB20-H3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D084_190204L12_exp180712_MS63_30nM_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L12_MS63_30nM_AB20-H3/2019-03-13-190204L12_MS63_30nM_AB20-H3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L12_MS63_30nM_AB20-H3/2019-03-13-190204L12_MS63_30nM_AB20-H3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D084_190204L12_exp180712_MS63_30nM_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L13_MS1_AB21-H4/2019-03-13-190204L13_MS1_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D085_190204L13_exp180712_MS01_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L13_MS1_AB21-H4/2019-03-13-190204L13_MS1_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L13_MS1_AB21-H4/2019-03-13-190204L13_MS1_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D085_190204L13_exp180712_MS01_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L14_MS80_AB21-H4/2019-03-13-190204L14_MS80_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D086_190204L14_exp180712_MS80_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L14_MS80_AB21-H4/2019-03-13-190204L14_MS80_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L14_MS80_AB21-H4/2019-03-13-190204L14_MS80_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D086_190204L14_exp180712_MS80_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L15_MS81_AB21-H4/2019-03-13-190204L15_MS81_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D087_190204L15_exp180712_MS81_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L15_MS81_AB21-H4/2019-03-13-190204L15_MS81_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L15_MS81_AB21-H4/2019-03-13-190204L15_MS81_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D087_190204L15_exp180712_MS81_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L16_MS63_0nM_AB21-H4/2019-03-13-190204L16_MS63_0nM_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D088_190204L16_exp180712_MS63_0nM_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L16_MS63_0nM_AB21-H4/2019-03-13-190204L16_MS63_0nM_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L16_MS63_0nM_AB21-H4/2019-03-13-190204L16_MS63_0nM_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D088_190204L16_exp180712_MS63_0nM_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L17_MS63_10nM_AB21-H4/2019-03-13-190204L17_MS63_10nM_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D089_190204L17_exp180712_MS63_10nM_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L17_MS63_10nM_AB21-H4/2019-03-13-190204L17_MS63_10nM_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L17_MS63_10nM_AB21-H4/2019-03-13-190204L17_MS63_10nM_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D089_190204L17_exp180712_MS63_10nM_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L18_MS63_30nM_AB21-H4/2019-03-13-190204L18_MS63_30nM_AB21-H4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D090_190204L18_exp180712_MS63_30nM_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L18_MS63_30nM_AB21-H4/2019-03-13-190204L18_MS63_30nM_AB21-H4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L18_MS63_30nM_AB21-H4/2019-03-13-190204L18_MS63_30nM_AB21-H4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D090_190204L18_exp180712_MS63_30nM_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L19_MS1_AB36-H3K9ac/2019-03-13-190204L19_MS1_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D091_190204L19_exp180712_MS01_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L19_MS1_AB36-H3K9ac/2019-03-13-190204L19_MS1_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L19_MS1_AB36-H3K9ac/2019-03-13-190204L19_MS1_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D091_190204L19_exp180712_MS01_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L20_MS80_AB36-H3K9ac/2019-03-13-190204L20_MS80_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D092_190204L20_exp180712_MS80_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L20_MS80_AB36-H3K9ac/2019-03-13-190204L20_MS80_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L20_MS80_AB36-H3K9ac/2019-03-13-190204L20_MS80_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D092_190204L20_exp180712_MS80_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L21_MS81_AB36-H3K9ac/2019-03-13-190204L21_MS81_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D093_190204L21_exp180712_MS81_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L21_MS81_AB36-H3K9ac/2019-03-13-190204L21_MS81_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L21_MS81_AB36-H3K9ac/2019-03-13-190204L21_MS81_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D093_190204L21_exp180712_MS81_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D094_190204L22_exp180712_MS63_0nM_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac/2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D094_190204L22_exp180712_MS63_0nM_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D095_190204L23_exp180712_MS63_10nM_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac/2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D095_190204L23_exp180712_MS63_10nM_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D096_190204L24_exp180712_MS63_30nM_AB36.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac/2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D096_190204L24_exp180712_MS63_30nM_AB36.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L25_MS1_AB37-H3K18ac/2019-03-13-190204L25_MS1_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D097_190204L25_exp180712_MS01_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L25_MS1_AB37-H3K18ac/2019-03-13-190204L25_MS1_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L25_MS1_AB37-H3K18ac/2019-03-13-190204L25_MS1_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D097_190204L25_exp180712_MS01_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L26_MS80_AB37-H3K18ac/2019-03-13-190204L26_MS80_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D098_190204L26_exp180712_MS80_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L26_MS80_AB37-H3K18ac/2019-03-13-190204L26_MS80_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L26_MS80_AB37-H3K18ac/2019-03-13-190204L26_MS80_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D098_190204L26_exp180712_MS80_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L27_MS81_AB37-H3K18ac/2019-03-13-190204L27_MS81_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D099_190204L27_exp180712_MS81_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L27_MS81_AB37-H3K18ac/2019-03-13-190204L27_MS81_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L27_MS81_AB37-H3K18ac/2019-03-13-190204L27_MS81_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D099_190204L27_exp180712_MS81_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D100_190204L28_exp180712_MS63_0nM_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac/2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D100_190204L28_exp180712_MS63_0nM_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D101_190204L29_exp180712_MS63_10nM_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac/2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D101_190204L29_exp180712_MS63_10nM_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D102_190204L30_exp180712_MS63_30nM_AB37.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac/2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D102_190204L30_exp180712_MS63_30nM_AB37.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L31_MS1_AB38-H3K27ac/2019-03-13-190204L31_MS1_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D103_190204L31_exp180712_MS01_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L31_MS1_AB38-H3K27ac/2019-03-13-190204L31_MS1_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L31_MS1_AB38-H3K27ac/2019-03-13-190204L31_MS1_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D103_190204L31_exp180712_MS01_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L32_MS80_AB38-H3K27ac/2019-03-13-190204L32_MS80_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D104_190204L32_exp180712_MS80_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L32_MS80_AB38-H3K27ac/2019-03-13-190204L32_MS80_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L32_MS80_AB38-H3K27ac/2019-03-13-190204L32_MS80_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D104_190204L32_exp180712_MS80_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L33_MS81_AB38-H3K27ac/2019-03-13-190204L33_MS81_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D105_190204L33_exp180712_MS81_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L33_MS81_AB38-H3K27ac/2019-03-13-190204L33_MS81_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L33_MS81_AB38-H3K27ac/2019-03-13-190204L33_MS81_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D105_190204L33_exp180712_MS81_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D106_190204L34_exp180712_MS63_0nM_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac/2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D106_190204L34_exp180712_MS63_0nM_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D107_190204L35_exp180712_MS63_10nM_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac/2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D107_190204L35_exp180712_MS63_10nM_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D108_190204L36_exp180712_MS63_30nM_AB38.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac/2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D108_190204L36_exp180712_MS63_30nM_AB38.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L37_MS1_AB40-H4K16ac/2019-03-13-190204L37_MS1_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D109_190204L37_exp180712_MS01_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L37_MS1_AB40-H4K16ac/2019-03-13-190204L37_MS1_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L37_MS1_AB40-H4K16ac/2019-03-13-190204L37_MS1_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D109_190204L37_exp180712_MS01_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L38_MS80_AB40-H4K16ac/2019-03-13-190204L38_MS80_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D110_190204L38_exp180712_MS80_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L38_MS80_AB40-H4K16ac/2019-03-13-190204L38_MS80_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L38_MS80_AB40-H4K16ac/2019-03-13-190204L38_MS80_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D110_190204L38_exp180712_MS80_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L39_MS81_AB40-H4K16ac/2019-03-13-190204L39_MS81_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D111_190204L39_exp180712_MS81_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L39_MS81_AB40-H4K16ac/2019-03-13-190204L39_MS81_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L39_MS81_AB40-H4K16ac/2019-03-13-190204L39_MS81_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D111_190204L39_exp180712_MS81_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D112_190204L40_exp180712_MS63_0nM_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac/2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D112_190204L40_exp180712_MS63_0nM_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D113_190204L41_exp180712_MS63_10nM_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac/2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D113_190204L41_exp180712_MS63_10nM_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D114_190204L42_exp180712_MS63_30nM_AB40.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac/2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D114_190204L42_exp180712_MS63_30nM_AB40.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L43_MS1_AB46-H4K79me3/2019-03-13-190204L43_MS1_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D115_190204L43_exp180712_MS01_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L43_MS1_AB46-H4K79me3/2019-03-13-190204L43_MS1_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L43_MS1_AB46-H4K79me3/2019-03-13-190204L43_MS1_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D115_190204L43_exp180712_MS01_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L44_MS80_AB46-H4K79me3/2019-03-13-190204L44_MS80_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D116_190204L44_exp180712_MS80_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L44_MS80_AB46-H4K79me3/2019-03-13-190204L44_MS80_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L44_MS80_AB46-H4K79me3/2019-03-13-190204L44_MS80_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D116_190204L44_exp180712_MS80_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L45_MS81_AB46-H4K79me3/2019-03-13-190204L45_MS81_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D117_190204L45_exp180712_MS81_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L45_MS81_AB46-H4K79me3/2019-03-13-190204L45_MS81_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L45_MS81_AB46-H4K79me3/2019-03-13-190204L45_MS81_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D117_190204L45_exp180712_MS81_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D118_190204L46_exp180712_MS63_0nM_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3/2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D118_190204L46_exp180712_MS63_0nM_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D119_190204L47_exp180712_MS63_10nM_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3/2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D119_190204L47_exp180712_MS63_10nM_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D120_190204L48_exp180712_MS63_30nM_AB46_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3/2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D120_190204L48_exp180712_MS63_30nM_AB46_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L49_MS1_AB48-H4K36me3/2019-03-13-190204L49_MS1_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D121_190204L49_exp180712_MS01_AB48_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L49_MS1_AB48-H4K36me3/2019-03-13-190204L49_MS1_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L49_MS1_AB48-H4K36me3/2019-03-13-190204L49_MS1_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D121_190204L49_exp180712_MS01_AB48_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L50_MS80_AB48-H4K36me3/2019-03-13-190204L50_MS80_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D122_190204L50_exp180712_MS80_AB48_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L50_MS80_AB48-H4K36me3/2019-03-13-190204L50_MS80_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L50_MS80_AB48-H4K36me3/2019-03-13-190204L50_MS80_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D122_190204L50_exp180712_MS80_AB48_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L51_MS81_AB48-H4K36me3/2019-03-13-190204L51_MS81_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D123_190204L51_exp180712_MS81_AB48_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L51_MS81_AB48-H4K36me3/2019-03-13-190204L51_MS81_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L51_MS81_AB48-H4K36me3/2019-03-13-190204L51_MS81_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D123_190204L51_exp180712_MS81_AB48_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D124_190204L52_exp180712_MS63_0nM_AB48R_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3/2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D124_190204L52_exp180712_MS63_0nM_AB48R_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D125_190204L53_exp180712_MS63_10nM_AB48_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3/2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D125_190204L53_exp180712_MS63_10nM_AB48_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D126_190204L54_exp180712_MS63_30nM_AB48_R.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3/2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D126_190204L54_exp180712_MS63_30nM_AB48_R.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a