python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L01_MS207_2_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 - 2019-12-03-191015L01_MS207_2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L02_MS208_2_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 - 2019-12-03-191015L02_MS208_2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L03_MS209_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 - 2019-12-03-191015L03_MS209_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L04_MS283_2_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 - 2019-12-03-191015L04_MS283_2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L05_MS286_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 - 2019-12-03-191015L05_MS286_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L06_MS287_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 - 2019-12-03-191015L06_MS287_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L07_MS288_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 - 2019-12-03-191015L07_MS288_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L08_MS289_2_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 - 2019-12-03-191015L08_MS289_2_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L09_MS207_2_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L09_MS207_2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L10_MS208_2_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L10_MS208_2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L11_MS209_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L11_MS209_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L12_MS283_2_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L12_MS283_2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L13_MS286_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L13_MS286_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L14_MS287_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L14_MS287_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L15_MS288_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L15_MS288_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L16_MS289_2_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L16_MS289_2_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L17_MS207_2_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L17_MS207_2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L18_MS208_2_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L18_MS208_2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L19_MS209_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L19_MS209_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L20_MS283_2_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L20_MS283_2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L21_MS286_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L21_MS286_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L22_MS287_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L22_MS287_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L23_MS288_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L23_MS288_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L24_MS289_2_AB21.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L24_MS289_2_AB21.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L25_MS207_2_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L25_MS207_2_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L26_MS208_2_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L26_MS208_2_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L27_MS209_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L27_MS209_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L28_MS283_2_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L28_MS283_2_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L29_MS286_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L29_MS286_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L30_MS287_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L30_MS287_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L31_MS288_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L31_MS288_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L32_MS289_2_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L32_MS289_2_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L33_MS207_2_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L33_MS207_2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L34_MS208_2_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L34_MS208_2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L35_MS209_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L35_MS209_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L36_MS283_2_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L36_MS283_2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L37_MS286_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L37_MS286_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L38_MS287_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L38_MS287_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L39_MS288_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L39_MS288_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L40_MS289_2_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L40_MS289_2_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L41_MS207_2_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L41_MS207_2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L42_MS208_2_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L42_MS208_2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L43_MS209_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L43_MS209_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L44_MS283_2_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L44_MS283_2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L45_MS286_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L45_MS286_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L46_MS287_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L46_MS287_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L47_MS288_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L47_MS288_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191015L48_MS289_2_AB04.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L48_MS289_2_AB04.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L01_MS207_1_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 - 2019-12-03-191020L01_MS207_1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L02_MS208_1_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 - 2019-12-03-191020L02_MS208_1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L03_MS281_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 - 2019-12-03-191020L03_MS281_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L04_MS282_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 - 2019-12-03-191020L04_MS282_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L04_MS283_1_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 - 2019-12-03-191020L04_MS283_1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L06_MS284_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 - 2019-12-03-191020L06_MS284_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L07_MS285_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 - 2019-12-03-191020L07_MS285_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L08_MS289_1_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 - 2019-12-03-191020L08_MS289_1_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L09_MS207_1_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L09_MS207_1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L10_MS208_1_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L10_MS208_1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L11_MS281_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L11_MS281_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L12_MS282_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L12_MS282_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L13_MS283_1_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L13_MS283_1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L14_MS284_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L14_MS284_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L15_MS285_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L15_MS285_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L16_MS289_1_AB01.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L16_MS289_1_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L17_MS207_1_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L17_MS207_1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L18_MS208_1_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L18_MS208_1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L19_MS281_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L19_MS281_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L20_MS282_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L20_MS282_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L21_MS283_1_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L21_MS283_1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L22_MS284_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L22_MS284_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L23_MS285_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L23_MS285_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L24_MS289_1_AB20.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L24_MS289_1_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L25_MS207_1_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L25_MS207_1_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L26_MS208_1_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L26_MS208_1_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L27_MS281_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L27_MS281_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L28_MS282_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L28_MS282_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L29_MS283_1_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L29_MS283_1_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L30_MS284_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L30_MS284_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L31_MS285_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L31_MS285_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191020L32_MS289_1_AB48.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L32_MS289_1_AB48.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_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 - 2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_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 - 2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_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 - 2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_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 - 2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_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 - 2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_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 - 2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_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 - 2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_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 - 2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L09_JK01_EMM4S-MS1_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 - 2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L10_JK05_EMM4S-MS1_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 - 2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L11_JK01_EMM-IL-MS1_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 - 2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 2019-12-03-191113L12_JK05_EMM-IL-MS1_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 - 2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L01_MS207_2_input.end1.fastq.gz 2019-12-03-191015L01_MS207_2_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 - 2019-12-03-191015L01_MS207_2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L02_MS208_2_input.end1.fastq.gz 2019-12-03-191015L02_MS208_2_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 - 2019-12-03-191015L02_MS208_2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L03_MS209_input.end1.fastq.gz 2019-12-03-191015L03_MS209_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 - 2019-12-03-191015L03_MS209_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L04_MS283_2_input.end1.fastq.gz 2019-12-03-191015L04_MS283_2_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 - 2019-12-03-191015L04_MS283_2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L05_MS286_input.end1.fastq.gz 2019-12-03-191015L05_MS286_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 - 2019-12-03-191015L05_MS286_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L06_MS287_input.end1.fastq.gz 2019-12-03-191015L06_MS287_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 - 2019-12-03-191015L06_MS287_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L07_MS288_input.end1.fastq.gz 2019-12-03-191015L07_MS288_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 - 2019-12-03-191015L07_MS288_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L08_MS289_2_input.end1.fastq.gz 2019-12-03-191015L08_MS289_2_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 - 2019-12-03-191015L08_MS289_2_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L09_MS207_2_AB20.end1.fastq.gz 2019-12-03-191015L09_MS207_2_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L09_MS207_2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L10_MS208_2_AB20.end1.fastq.gz 2019-12-03-191015L10_MS208_2_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L10_MS208_2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L11_MS209_AB20.end1.fastq.gz 2019-12-03-191015L11_MS209_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L11_MS209_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L12_MS283_2_AB20.end1.fastq.gz 2019-12-03-191015L12_MS283_2_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L12_MS283_2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L13_MS286_AB20.end1.fastq.gz 2019-12-03-191015L13_MS286_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L13_MS286_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L14_MS287_AB20.end1.fastq.gz 2019-12-03-191015L14_MS287_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L14_MS287_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L15_MS288_AB20.end1.fastq.gz 2019-12-03-191015L15_MS288_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L15_MS288_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L16_MS289_2_AB20.end1.fastq.gz 2019-12-03-191015L16_MS289_2_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L16_MS289_2_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L17_MS207_2_AB21.end1.fastq.gz 2019-12-03-191015L17_MS207_2_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L17_MS207_2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L18_MS208_2_AB21.end1.fastq.gz 2019-12-03-191015L18_MS208_2_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L18_MS208_2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L19_MS209_AB21.end1.fastq.gz 2019-12-03-191015L19_MS209_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L19_MS209_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L20_MS283_2_AB21.end1.fastq.gz 2019-12-03-191015L20_MS283_2_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L20_MS283_2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L21_MS286_AB21.end1.fastq.gz 2019-12-03-191015L21_MS286_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L21_MS286_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L22_MS287_AB21.end1.fastq.gz 2019-12-03-191015L22_MS287_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L22_MS287_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L23_MS288_AB21.end1.fastq.gz 2019-12-03-191015L23_MS288_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L23_MS288_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L24_MS289_2_AB21.end1.fastq.gz 2019-12-03-191015L24_MS289_2_AB21.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L24_MS289_2_AB21.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L25_MS207_2_AB48.end1.fastq.gz 2019-12-03-191015L25_MS207_2_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L25_MS207_2_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L26_MS208_2_AB48.end1.fastq.gz 2019-12-03-191015L26_MS208_2_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L26_MS208_2_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L27_MS209_AB48.end1.fastq.gz 2019-12-03-191015L27_MS209_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L27_MS209_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L28_MS283_2_AB48.end1.fastq.gz 2019-12-03-191015L28_MS283_2_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L28_MS283_2_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L29_MS286_AB48.end1.fastq.gz 2019-12-03-191015L29_MS286_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L29_MS286_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L30_MS287_AB48.end1.fastq.gz 2019-12-03-191015L30_MS287_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L30_MS287_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L31_MS288_AB48.end1.fastq.gz 2019-12-03-191015L31_MS288_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L31_MS288_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L32_MS289_2_AB48.end1.fastq.gz 2019-12-03-191015L32_MS289_2_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L32_MS289_2_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L33_MS207_2_AB01.end1.fastq.gz 2019-12-03-191015L33_MS207_2_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L33_MS207_2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L34_MS208_2_AB01.end1.fastq.gz 2019-12-03-191015L34_MS208_2_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L34_MS208_2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L35_MS209_AB01.end1.fastq.gz 2019-12-03-191015L35_MS209_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L35_MS209_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L36_MS283_2_AB01.end1.fastq.gz 2019-12-03-191015L36_MS283_2_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L36_MS283_2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L37_MS286_AB01.end1.fastq.gz 2019-12-03-191015L37_MS286_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L37_MS286_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L38_MS287_AB01.end1.fastq.gz 2019-12-03-191015L38_MS287_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L38_MS287_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L39_MS288_AB01.end1.fastq.gz 2019-12-03-191015L39_MS288_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L39_MS288_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L40_MS289_2_AB01.end1.fastq.gz 2019-12-03-191015L40_MS289_2_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191015L40_MS289_2_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L41_MS207_2_AB04.end1.fastq.gz 2019-12-03-191015L41_MS207_2_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L41_MS207_2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L42_MS208_2_AB04.end1.fastq.gz 2019-12-03-191015L42_MS208_2_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L42_MS208_2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L43_MS209_AB04.end1.fastq.gz 2019-12-03-191015L43_MS209_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L43_MS209_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L44_MS283_2_AB04.end1.fastq.gz 2019-12-03-191015L44_MS283_2_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L44_MS283_2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L45_MS286_AB04.end1.fastq.gz 2019-12-03-191015L45_MS286_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L45_MS286_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L46_MS287_AB04.end1.fastq.gz 2019-12-03-191015L46_MS287_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L46_MS287_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L47_MS288_AB04.end1.fastq.gz 2019-12-03-191015L47_MS288_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L47_MS288_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191015L48_MS289_2_AB04.end1.fastq.gz 2019-12-03-191015L48_MS289_2_AB04.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191015L48_MS289_2_AB04.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L01_MS207_1_input.end1.fastq.gz 2019-12-03-191020L01_MS207_1_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 - 2019-12-03-191020L01_MS207_1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L02_MS208_1_input.end1.fastq.gz 2019-12-03-191020L02_MS208_1_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 - 2019-12-03-191020L02_MS208_1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L03_MS281_input.end1.fastq.gz 2019-12-03-191020L03_MS281_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 - 2019-12-03-191020L03_MS281_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L04_MS282_input.end1.fastq.gz 2019-12-03-191020L04_MS282_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 - 2019-12-03-191020L04_MS282_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L04_MS283_1_input.end1.fastq.gz 2019-12-03-191020L04_MS283_1_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 - 2019-12-03-191020L04_MS283_1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L06_MS284_input.end1.fastq.gz 2019-12-03-191020L06_MS284_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 - 2019-12-03-191020L06_MS284_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L07_MS285_input.end1.fastq.gz 2019-12-03-191020L07_MS285_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 - 2019-12-03-191020L07_MS285_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L08_MS289_1_input.end1.fastq.gz 2019-12-03-191020L08_MS289_1_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 - 2019-12-03-191020L08_MS289_1_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L09_MS207_1_AB01.end1.fastq.gz 2019-12-03-191020L09_MS207_1_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L09_MS207_1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L10_MS208_1_AB01.end1.fastq.gz 2019-12-03-191020L10_MS208_1_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L10_MS208_1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L11_MS281_AB01.end1.fastq.gz 2019-12-03-191020L11_MS281_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L11_MS281_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L12_MS282_AB01.end1.fastq.gz 2019-12-03-191020L12_MS282_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L12_MS282_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L13_MS283_1_AB01.end1.fastq.gz 2019-12-03-191020L13_MS283_1_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L13_MS283_1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L14_MS284_AB01.end1.fastq.gz 2019-12-03-191020L14_MS284_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L14_MS284_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L15_MS285_AB01.end1.fastq.gz 2019-12-03-191020L15_MS285_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L15_MS285_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L16_MS289_1_AB01.end1.fastq.gz 2019-12-03-191020L16_MS289_1_AB01.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - 2019-12-03-191020L16_MS289_1_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L17_MS207_1_AB20.end1.fastq.gz 2019-12-03-191020L17_MS207_1_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L17_MS207_1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L18_MS208_1_AB20.end1.fastq.gz 2019-12-03-191020L18_MS208_1_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L18_MS208_1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L19_MS281_AB20.end1.fastq.gz 2019-12-03-191020L19_MS281_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L19_MS281_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L20_MS282_AB20.end1.fastq.gz 2019-12-03-191020L20_MS282_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L20_MS282_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L21_MS283_1_AB20.end1.fastq.gz 2019-12-03-191020L21_MS283_1_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L21_MS283_1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L22_MS284_AB20.end1.fastq.gz 2019-12-03-191020L22_MS284_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L22_MS284_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L23_MS285_AB20.end1.fastq.gz 2019-12-03-191020L23_MS285_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L23_MS285_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L24_MS289_1_AB20.end1.fastq.gz 2019-12-03-191020L24_MS289_1_AB20.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L24_MS289_1_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L25_MS207_1_AB48.end1.fastq.gz 2019-12-03-191020L25_MS207_1_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L25_MS207_1_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L26_MS208_1_AB48.end1.fastq.gz 2019-12-03-191020L26_MS208_1_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L26_MS208_1_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L27_MS281_AB48.end1.fastq.gz 2019-12-03-191020L27_MS281_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L27_MS281_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L28_MS282_AB48.end1.fastq.gz 2019-12-03-191020L28_MS282_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L28_MS282_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L29_MS283_1_AB48.end1.fastq.gz 2019-12-03-191020L29_MS283_1_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L29_MS283_1_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L30_MS284_AB48.end1.fastq.gz 2019-12-03-191020L30_MS284_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L30_MS284_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L31_MS285_AB48.end1.fastq.gz 2019-12-03-191020L31_MS285_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L31_MS285_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191020L32_MS289_1_AB48.end1.fastq.gz 2019-12-03-191020L32_MS289_1_AB48.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+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 - 2019-12-03-191020L32_MS289_1_AB48.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.end1.fastq.gz 2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_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 - 2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.end1.fastq.gz 2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_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 - 2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.end1.fastq.gz 2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_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 - 2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.end1.fastq.gz 2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_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 - 2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.end1.fastq.gz 2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_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 - 2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.end1.fastq.gz 2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_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 - 2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.end1.fastq.gz 2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_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 - 2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.end1.fastq.gz 2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_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 - 2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.end1.fastq.gz 2019-12-03-191113L09_JK01_EMM4S-MS1_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 - 2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.end1.fastq.gz 2019-12-03-191113L10_JK05_EMM4S-MS1_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 - 2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.end1.fastq.gz 2019-12-03-191113L11_JK01_EMM-IL-MS1_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 - 2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.end1.fastq.gz 2019-12-03-191113L12_JK05_EMM-IL-MS1_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 - 2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a