python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L01_MS1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L02_MS80_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L03_MS81_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L04_MS63_0nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L05_MS63_10nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L06_MS63_30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L07_MS1_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L08_MS80_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L09_MS81_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L10_MS63_0nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L11_MS63_10nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L12_MS63_30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L13_MS1_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L14_MS80_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L15_MS81_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L16_MS63_0nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L17_MS63_10nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L18_MS63_30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L19_MS1_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L20_MS80_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L21_MS81_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L25_MS1_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L26_MS80_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L27_MS81_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L31_MS1_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L32_MS80_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L33_MS81_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L37_MS1_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L38_MS80_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L39_MS81_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L43_MS1_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L44_MS80_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L45_MS81_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L49_MS1_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L50_MS80_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L51_MS81_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L01_MS430_0nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L01_MS430_0nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L02_MS430_10nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L02_MS430_10nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L03_MS430_30nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L03_MS430_30nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L04_MS431_0nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L04_MS431_0nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L05_MS431_10nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L05_MS431_10nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L06_MS431_30nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L06_MS431_30nM-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L07_MS1-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L07_MS1-sp110-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L08_MS434_0nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L08_MS434_0nM-sp113-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L09_MS434_10nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L09_MS434_10nM-sp113-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L10_MS434_30nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L10_MS434_30nM-sp113-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L11_MS1-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L11_MS1-sp113-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L12_MS1-sp112-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L12_MS1-sp112-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L13_MS435_0nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L13_MS435_0nM-sp114-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L14_MS435_10nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L14_MS435_10nM-sp114-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L15_MS435_30nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L15_MS435_30nM-sp114-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L16_MS1-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L16_MS1-sp114-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L17_MS437_0nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L17_MS437_0nM-sp116-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L18_MS437_10nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L18_MS437_10nM-sp116-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L19_MS437_30nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L19_MS437_30nM-sp116-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L20_MS1-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L20_MS1-sp116-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L21_MS437B_0nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L21_MS437B_0nM-sp115-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L22_MS437B_10nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L22_MS437B_10nM-sp115-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L23_MS437B_30nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L23_MS437B_30nM-sp115-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L24_MS1-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L24_MS1-sp115-input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L31_MS1-sp110-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L31_MS1-sp110-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L35_MS1-sp113-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L35_MS1-sp113-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L36_MS1-sp112_A-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L36_MS1-sp112_A-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L37_MS1-sp112_B-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L37_MS1-sp112_B-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L41_MS1-sp114-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L41_MS1-sp114-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L45_MS1-sp116-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L45_MS1-sp116-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L49_MS1-sp115-AB101.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L49_MS1-sp115-AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L56_MS1-sp110-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L56_MS1-sp110-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L60_MS1-sp113-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L60_MS1-sp113-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L61_MS1-sp112_A-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L61_MS1-sp112_A-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L62_MS1-sp112_B-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L62_MS1-sp112_B-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L66_MSMS1-sp114-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L66_MSMS1-sp114-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L70_MS1-sp116-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L70_MS1-sp116-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L74_MS1-sp115-AB107.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L74_MS1-sp115-AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L01_MS1_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L01_MS1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L02_MS80_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L02_MS80_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L03_MS81_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L03_MS81_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L04_MS63_0nM_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L04_MS63_0nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L05_MS63_10nM_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L05_MS63_10nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-181105L06_MS63_30nM_input.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-181105L06_MS63_30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L07_MS1_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L07_MS1_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L08_MS80_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L08_MS80_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L09_MS81_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L09_MS81_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L10_MS63_0nM_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L10_MS63_0nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L11_MS63_10nM_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L11_MS63_10nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L12_MS63_30nM_AB20-H3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L12_MS63_30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L13_MS1_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L13_MS1_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L14_MS80_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L14_MS80_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L15_MS81_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L15_MS81_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L16_MS63_0nM_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L16_MS63_0nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L17_MS63_10nM_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L17_MS63_10nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L18_MS63_30nM_AB21-H4.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L18_MS63_30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L19_MS1_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L19_MS1_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L20_MS80_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L20_MS80_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L21_MS81_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L21_MS81_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L22_MS63_0nM_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L23_MS63_10nM_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L24_MS63_30nM_AB36-H3K9ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L25_MS1_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L25_MS1_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L26_MS80_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L26_MS80_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L27_MS81_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L27_MS81_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L28_MS63_0nM_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L29_MS63_10nM_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L30_MS63_30nM_AB37-H3K18ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L31_MS1_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L31_MS1_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L32_MS80_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L32_MS80_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L33_MS81_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L33_MS81_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L34_MS63_0nM_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L35_MS63_10nM_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L36_MS63_30nM_AB38-H3K27ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L37_MS1_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L37_MS1_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L38_MS80_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L38_MS80_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L39_MS81_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L39_MS81_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L40_MS63_0nM_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L41_MS63_10nM_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L42_MS63_30nM_AB40-H4K16ac.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L43_MS1_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L43_MS1_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L44_MS80_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L44_MS80_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L45_MS81_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L45_MS81_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L46_MS63_0nM_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L47_MS63_10nM_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L48_MS63_30nM_AB46-H4K79me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L49_MS1_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L49_MS1_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L50_MS80_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L50_MS80_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L51_MS81_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L51_MS81_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L52_MS63_0nM_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L53_MS63_10nM_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.end1.fastq.gz 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 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190204L54_MS63_30nM_AB48-H4K36me3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L01_MS430_0nM-sp110-input.end1.fastq.gz 2019-03-13-190218L01_MS430_0nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L01_MS430_0nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L02_MS430_10nM-sp110-input.end1.fastq.gz 2019-03-13-190218L02_MS430_10nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L02_MS430_10nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L03_MS430_30nM-sp110-input.end1.fastq.gz 2019-03-13-190218L03_MS430_30nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L03_MS430_30nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L04_MS431_0nM-sp110-input.end1.fastq.gz 2019-03-13-190218L04_MS431_0nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L04_MS431_0nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L05_MS431_10nM-sp110-input.end1.fastq.gz 2019-03-13-190218L05_MS431_10nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L05_MS431_10nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L06_MS431_30nM-sp110-input.end1.fastq.gz 2019-03-13-190218L06_MS431_30nM-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L06_MS431_30nM-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L07_MS1-sp110-input.end1.fastq.gz 2019-03-13-190218L07_MS1-sp110-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L07_MS1-sp110-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L08_MS434_0nM-sp113-input.end1.fastq.gz 2019-03-13-190218L08_MS434_0nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L08_MS434_0nM-sp113-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L09_MS434_10nM-sp113-input.end1.fastq.gz 2019-03-13-190218L09_MS434_10nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L09_MS434_10nM-sp113-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L10_MS434_30nM-sp113-input.end1.fastq.gz 2019-03-13-190218L10_MS434_30nM-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L10_MS434_30nM-sp113-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L11_MS1-sp113-input.end1.fastq.gz 2019-03-13-190218L11_MS1-sp113-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L11_MS1-sp113-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L12_MS1-sp112-input.end1.fastq.gz 2019-03-13-190218L12_MS1-sp112-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L12_MS1-sp112-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L13_MS435_0nM-sp114-input.end1.fastq.gz 2019-03-13-190218L13_MS435_0nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L13_MS435_0nM-sp114-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L14_MS435_10nM-sp114-input.end1.fastq.gz 2019-03-13-190218L14_MS435_10nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L14_MS435_10nM-sp114-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L15_MS435_30nM-sp114-input.end1.fastq.gz 2019-03-13-190218L15_MS435_30nM-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L15_MS435_30nM-sp114-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L16_MS1-sp114-input.end1.fastq.gz 2019-03-13-190218L16_MS1-sp114-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L16_MS1-sp114-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L17_MS437_0nM-sp116-input.end1.fastq.gz 2019-03-13-190218L17_MS437_0nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L17_MS437_0nM-sp116-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L18_MS437_10nM-sp116-input.end1.fastq.gz 2019-03-13-190218L18_MS437_10nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L18_MS437_10nM-sp116-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L19_MS437_30nM-sp116-input.end1.fastq.gz 2019-03-13-190218L19_MS437_30nM-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L19_MS437_30nM-sp116-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L20_MS1-sp116-input.end1.fastq.gz 2019-03-13-190218L20_MS1-sp116-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L20_MS1-sp116-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L21_MS437B_0nM-sp115-input.end1.fastq.gz 2019-03-13-190218L21_MS437B_0nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L21_MS437B_0nM-sp115-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L22_MS437B_10nM-sp115-input.end1.fastq.gz 2019-03-13-190218L22_MS437B_10nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L22_MS437B_10nM-sp115-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L23_MS437B_30nM-sp115-input.end1.fastq.gz 2019-03-13-190218L23_MS437B_30nM-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L23_MS437B_30nM-sp115-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L24_MS1-sp115-input.end1.fastq.gz 2019-03-13-190218L24_MS1-sp115-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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L24_MS1-sp115-input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.end1.fastq.gz 2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.end1.fastq.gz 2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.end1.fastq.gz 2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.end1.fastq.gz 2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.end1.fastq.gz 2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.end1.fastq.gz 2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L31_MS1-sp110-AB101.end1.fastq.gz 2019-03-13-190218L31_MS1-sp110-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.end1.fastq.gz 2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.end1.fastq.gz 2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.end1.fastq.gz 2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L35_MS1-sp113-AB101.end1.fastq.gz 2019-03-13-190218L35_MS1-sp113-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L36_MS1-sp112_A-AB101.end1.fastq.gz 2019-03-13-190218L36_MS1-sp112_A-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L37_MS1-sp112_B-AB101.end1.fastq.gz 2019-03-13-190218L37_MS1-sp112_B-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.end1.fastq.gz 2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.end1.fastq.gz 2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.end1.fastq.gz 2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L41_MS1-sp114-AB101.end1.fastq.gz 2019-03-13-190218L41_MS1-sp114-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L45_MS1-sp116-AB101.end1.fastq.gz 2019-03-13-190218L45_MS1-sp116-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L49_MS1-sp115-AB101.end1.fastq.gz 2019-03-13-190218L49_MS1-sp115-AB101.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L56_MS1-sp110-AB107.end1.fastq.gz 2019-03-13-190218L56_MS1-sp110-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L60_MS1-sp113-AB107.end1.fastq.gz 2019-03-13-190218L60_MS1-sp113-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L61_MS1-sp112_A-AB107.end1.fastq.gz 2019-03-13-190218L61_MS1-sp112_A-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L62_MS1-sp112_B-AB107.end1.fastq.gz 2019-03-13-190218L62_MS1-sp112_B-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L66_MSMS1-sp114-AB107.end1.fastq.gz 2019-03-13-190218L66_MSMS1-sp114-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L70_MS1-sp116-AB107.end1.fastq.gz 2019-03-13-190218L70_MS1-sp116-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.end1.fastq.gz 2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L74_MS1-sp115-AB107.end1.fastq.gz 2019-03-13-190218L74_MS1-sp115-AB107.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.end1.fastq.gz 2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.end1.fastq.gz 2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.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+Schizosaccharomyces_pombe.ASM294v2.20 -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a