python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Input-180525_L1/2018-06-16-MS1-Input-180525_L1.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B001_180525L01_exp180222_MS01_SCGE_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Input-180525_L1/2018-06-16-MS1-Input-180525_L1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Input-180525_L1/2018-06-16-MS1-Input-180525_L1.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B001_180525L01_exp180222_MS01_SCGE_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Pol2-180525_L4/2018-06-16-MS1-Pol2-180525_L4.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B007_180525L04_exp180222_MS01_SCGE_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Pol2-180525_L4/2018-06-16-MS1-Pol2-180525_L4.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-Pol2-180525_L4/2018-06-16-MS1-Pol2-180525_L4.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B007_180525L04_exp180222_MS01_SCGE_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS2-180525_L7/2018-06-16-MS1-RNAPII_pS2-180525_L7.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B013_180525L07_exp180222_MS01_SCGE_AB02.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS2-180525_L7/2018-06-16-MS1-RNAPII_pS2-180525_L7.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS2-180525_L7/2018-06-16-MS1-RNAPII_pS2-180525_L7.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B013_180525L07_exp180222_MS01_SCGE_AB02.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS5-180525_L10/2018-06-16-MS1-RNAPII_pS5-180525_L10.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B019_180525L10_exp180222_MS01_SCGE_AB05.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS5-180525_L10/2018-06-16-MS1-RNAPII_pS5-180525_L10.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-RNAPII_pS5-180525_L10/2018-06-16-MS1-RNAPII_pS5-180525_L10.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B019_180525L10_exp180222_MS01_SCGE_AB05.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-H3-180525_L13/2018-06-16-MS1-H3-180525_L13.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B025_180525L13_exp180222_MS01_SCGE_AB20.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-H3-180525_L13/2018-06-16-MS1-H3-180525_L13.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-06-16-MS1-H3-180525_L13/2018-06-16-MS1-H3-180525_L13.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes -p 20 -v 2 -a -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - B025_180525L13_exp180222_MS01_SCGE_AB20.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a