python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L02_exp201015_MS214_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L02_exp201015_MS214_SCGE_RAPA-10min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L02_exp201015_MS214_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L02_exp201015_MS214_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L02_exp201015_MS214_SCGE_RAPA-10min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L03_exp201015_MS214_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L03_exp201015_MS214_SCGE_RAPA-20min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L03_exp201015_MS214_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L03_exp201015_MS214_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L03_exp201015_MS214_SCGE_RAPA-20min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L04_exp201015_MS214_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L04_exp201015_MS214_SCGE_RAPA-40min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L04_exp201015_MS214_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L04_exp201015_MS214_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L04_exp201015_MS214_SCGE_RAPA-40min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA_2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L05_exp201015_MS214_SCGE_RAPA-60min_DNA_2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA_2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L06_exp201015_MS214_SCGE_RAPA-90min_DNA_2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA_2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L07_exp201015_MS215_SCGE_RAPA-00min_DNA_2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA_2.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA_2.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L08_exp201015_MS215_SCGE_RAPA-10min_DNA_2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L09_exp201015_MS215_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L09_exp201015_MS215_SCGE_RAPA-20min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L09_exp201015_MS215_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L09_exp201015_MS215_SCGE_RAPA-20min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L09_exp201015_MS215_SCGE_RAPA-20min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L10_exp201015_MS215_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L10_exp201015_MS215_SCGE_RAPA-40min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L10_exp201015_MS215_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L10_exp201015_MS215_SCGE_RAPA-40min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L10_exp201015_MS215_SCGE_RAPA-40min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L11_exp201015_MS215_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L11_exp201015_MS215_SCGE_RAPA-60min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L11_exp201015_MS215_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L11_exp201015_MS215_SCGE_RAPA-60min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L11_exp201015_MS215_SCGE_RAPA-60min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L12_exp201015_MS215_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L12_exp201015_MS215_SCGE_RAPA-90min_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L12_exp201015_MS215_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L12_exp201015_MS215_SCGE_RAPA-90min_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L12_exp201015_MS215_SCGE_RAPA-90min_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L13_exp201126_MS31_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L13_exp201126_MS31_SCGE-URA_4min-4TU_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L13_exp201126_MS31_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L13_exp201126_MS31_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L13_exp201126_MS31_SCGE-URA_4min-4TU_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L14_exp201126_MS32_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L14_exp201126_MS32_SCGE-URA_4min-4TU_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L14_exp201126_MS32_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L14_exp201126_MS32_SCGE-URA_4min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L14_exp201126_MS32_SCGE-URA_4min-4TU_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L15_exp201126_MS31_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L15_exp201126_MS31_SCGE-URA_10min-4TU_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L15_exp201126_MS31_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L15_exp201126_MS31_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L15_exp201126_MS31_SCGE-URA_10min-4TU_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py 210121L16_exp201126_MS32_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /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 - 210121L16_exp201126_MS32_SCGE-URA_10min-4TU_DNA.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 210121L16_exp201126_MS32_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 210121L16_exp201126_MS32_SCGE-URA_10min-4TU_DNA.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /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 - 210121L16_exp201126_MS32_SCGE-URA_10min-4TU_DNA.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L1979-210117L05_GM16_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L1979-210117L05_GM16_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz L1979-210117L05_GM16_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1979-210117L05_GM16_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L1980-210117L06_GM17_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L1980-210117L06_GM17_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz L1980-210117L06_GM17_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1980-210117L06_GM17_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L1981-210117L07_GM18_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L1981-210117L07_GM18_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz L1981-210117L07_GM18_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1981-210117L07_GM18_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L1982-210117L08_GM19_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L1982-210117L08_GM19_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end1.fastq.gz L1982-210117L08_GM19_SC-RAF-GAL_AB03.210130_NB551514_0540_AHKHVWBGXH.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L1982-210117L08_GM19_SC-RAF-GAL_AB03.2x36mers.sacCer3.unique