mkdir /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2023-12-07-Anupama-olfactory
cd /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2023-12-07-Anupama-olfactory
==================================================================================
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE240023
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512111 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512105 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512104 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512099 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512100 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512098 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512097 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512096 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512101 --split-spot --split-files --threads 20 -O mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512107	--split-spot --split-files --threads 20 -O OMP-GFP_ATAC_rep1-GSM7679975
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512106 --split-spot --split-files --threads 20 -O OMP-GFP_ATAC_rep2-GSM7679976
/oak/stanford/groups/akundaje/marinovg/programs/sratoolkit.2.11.0-ubuntu64/bin/fasterq-dump SRR25512103 --split-spot --split-files --threads 20 -O OMP-GFP_ATAC_rep3-GSM7679977
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 16 20000 24:00:00 normal,akundaje,owners,sfgf zFQD1
==================================================================================
ls -1 */* > z
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end2.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956/*_1.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end1.fastq.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956/*_2.fastq | gzip > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end2.fastq.gz
cat OMP-GFP_ATAC_rep1-GSM7679975/*_1.fastq | gzip > OMP-GFP_ATAC_rep1-GSM7679975.end1.fastq.gz
cat OMP-GFP_ATAC_rep1-GSM7679975/*_2.fastq | gzip > OMP-GFP_ATAC_rep1-GSM7679975.end2.fastq.gz
cat OMP-GFP_ATAC_rep2-GSM7679976/*_1.fastq | gzip > OMP-GFP_ATAC_rep2-GSM7679976.end1.fastq.gz
cat OMP-GFP_ATAC_rep2-GSM7679976/*_2.fastq | gzip > OMP-GFP_ATAC_rep2-GSM7679976.end2.fastq.gz
cat OMP-GFP_ATAC_rep3-GSM7679977/*_1.fastq | gzip > OMP-GFP_ATAC_rep3-GSM7679977.end1.fastq.gz
cat OMP-GFP_ATAC_rep3-GSM7679977/*_2.fastq | gzip > OMP-GFP_ATAC_rep3-GSM7679977.end2.fastq.gz
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 24:00:00 normal,akundaje,owners,sfgf zGZ
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955
rm -r mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956
rm -r OMP-GFP_ATAC_rep1-GSM7679975
rm -r OMP-GFP_ATAC_rep2-GSM7679976
rm -r OMP-GFP_ATAC_rep3-GSM7679977
zcat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.fastq.lines
zcat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end1.fastq.gz | wc -l > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.fastq.lines
zcat OMP-GFP_ATAC_rep1-GSM7679975.end1.fastq.gz | wc -l > OMP-GFP_ATAC_rep1-GSM7679975.fastq.lines
zcat OMP-GFP_ATAC_rep2-GSM7679976.end1.fastq.gz | wc -l > OMP-GFP_ATAC_rep2-GSM7679976.fastq.lines
zcat OMP-GFP_ATAC_rep3-GSM7679977.end1.fastq.gz | wc -l > OMP-GFP_ATAC_rep3-GSM7679977.fastq.lines
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 10:00:00 akundaje,normal,owners,sfgf zCL
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep1-GSM7679975.end1.fastq.gz OMP-GFP_ATAC_rep1-GSM7679975.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep2-GSM7679976.end1.fastq.gz OMP-GFP_ATAC_rep2-GSM7679976.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep3-GSM7679977.end1.fastq.gz OMP-GFP_ATAC_rep3-GSM7679977.end2.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/mm10/bowtie-indexes/chrM -p 20 -v 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/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10-chrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end1.fastq.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep1-GSM7679975.end1.fastq.gz OMP-GFP_ATAC_rep1-GSM7679975.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep2-GSM7679976.end1.fastq.gz OMP-GFP_ATAC_rep2-GSM7679976.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py OMP-GFP_ATAC_rep3-GSM7679977.end1.fastq.gz OMP-GFP_ATAC_rep3-GSM7679977.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.2.2-linux-x86_64/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --12 - | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 8 50000 24:00:00 akundaje,normal,owners,sfgf zMAP
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.bam OUTPUT=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.bam OUTPUT=OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.bam OUTPUT=OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.bam OUTPUT=OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam METRICS_FILE=OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.metrics VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true &
module load java; 
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 10:00:00 akundaje,normal,owners,sfgf zMD
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10-chrM.bam
samtools index OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10-chrM.bam
samtools index OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10-chrM.bam
samtools index OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10-chrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.bam
samtools index OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.bam
samtools index OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.bam
samtools index OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam
samtools index OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 10:00:00 akundaje,normal,owners,sfgf zI
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10-chrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10-chrM.bam SAMstats-OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10-chrM.bam SAMstats-OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10-chrM.bam SAMstats-OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10-chrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.bam SAMstats-OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.bam SAMstats-OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.bam SAMstats-OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam SAMstats-OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.wig -notitle -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.InsLen -uniqueBAM -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 50000 48:00:00 akundaje,normal,owners,sfgf zMW
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.wig /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bigWig
ml system libpng/1.2.57; 
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 1:00:00 akundaje,normal,owners,sfgf zBW
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bigWig mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bigWig OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bigWig OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/signalAroundCoordinate-BW.py /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10-refFlat-2014-10-26.TSS-0bp.bed 0 1 3 4000 OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bigWig OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.TSS_profile -normalize &
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf ztss
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
python /oak/stanford/groups/akundaje/marinovg/code/ATAC/ATACTSSscore.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.TSS_profile 100 2000 >> ATACTSSscore.txt
module load viz; module load py-matplotlib/2.2.2_py27; module load py-scipy/1.1.0_py27; module load R/3.5.1;
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.InsLen mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956 fragment_length 0 fragment_count 1 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.InsLen OMP-GFP_ATAC_rep1-GSM7679975 fragment_length 0 fragment_count 1 OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.InsLen OMP-GFP_ATAC_rep2-GSM7679976 fragment_length 0 fragment_count 1 OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python ~/code/plotting/XY.py OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.InsLen OMP-GFP_ATAC_rep3-GSM7679977 fragment_length 0 fragment_count 1 OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.InsLen.png -xlimits 0 800
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 1:00:00 akundaje,normal,owners,sfgf zXY
mkdir png
cp *.png png
rm *.wig
rm *.unique.bam
rm *.unique.bam.bai
rm *.unique.nochrM.bam
rm *.unique.nochrM.bam.bai
rm *.fastq.gz
python ~/code/SAMstats-table.py SAMstats.files SAMstats.table
mkdir SAMstats_files
mv SAMstats-* SAMstats_files
tar -czvf SAMstats_files.tar.gz SAMstats_files
rm -r SAMstats_files
...................................
~/programs/samtools-0.1.19/samtools merge -f mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam
~/programs/samtools-0.1.19/samtools merge -f mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam
~/programs/samtools-0.1.19/samtools merge -f OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.bam OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam
~/programs/samtools-0.1.19/samtools merge -f mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf zSM
~/programs/samtools-0.1.18/samtools sort mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted &
~/programs/samtools-0.1.18/samtools sort mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted &
~/programs/samtools-0.1.18/samtools sort OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.bam OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted &
~/programs/samtools-0.1.18/samtools sort mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.bam mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted &
python ~/code/SLURM.py z 1 10000 10:00:00 akundaje,normal,owners,sfgf zSS
rm mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.bam
rm mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.bam
rm OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.bam
rm mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.bam
rm *mm10-chrM.bam
rm *mm10-chrM.bam.bai
rm *mm10.unique.nochrM.bam
rm *mm10.unique.nochrM.bam.bai
python ~/code/BAMPseudoReps-V2.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.bam ~/programs/samtools-0.1.18/samtools ~/genomes/mm10/sequence/mm10.fa
python ~/code/BAMPseudoReps-V2.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.bam ~/programs/samtools-0.1.18/samtools ~/genomes/mm10/sequence/mm10.fa
python ~/code/BAMPseudoReps-V2.py OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.bam ~/programs/samtools-0.1.18/samtools ~/genomes/mm10/sequence/mm10.fa
python ~/code/BAMPseudoReps-V2.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.bam ~/programs/samtools-0.1.18/samtools ~/genomes/mm10/sequence/mm10.fa
python ~/code/SLURM.py z 1 10000 10:00:00 akundaje,normal,owners,sfgf zBPR
ls -1 *.bam > z
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep1.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep2.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep1.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep2.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep1.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep2.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam -n mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.bam -n OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep1.bam -n OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep2.bam -n OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam -n OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam -n OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
/oak/stanford/groups/akundaje/marinovg/programs/MACS-2.1.0/bin/macs2 callpeak -t OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam -n OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1 -g hs -f BAMPE --to-large -p 1e-1 --keep-dup all --nomodel
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf zMACS
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
cat OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak | sort -k 8nr,8nr | awk 'BEGIN{OFS="	"}{$4="Peak_"NR ; print $0}' | head -300000 | gzip -c > OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf zSORT
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep2-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep2-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep2-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep2-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep2-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep2-vs-rep3-IDR --peak-list  mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep1.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.pseudoRep2.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file OMP-GFP_ATAC.pseudoreps.IDR --peak-list  OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file OMP-GFP_ATAC.rep1-vs-rep2-IDR --peak-list  OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file OMP-GFP_ATAC.rep1-vs-rep3-IDR --peak-list  OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
module load idr/latest; /oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4.2/bin/idr --samples OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --input-file-type narrowPeak --output-file OMP-GFP_ATAC.rep2-vs-rep3-IDR --peak-list  OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.merged.sorted.MACS-2.1.0.p1e-1_peaks.narrowPeak.sorted.300K.gz --rank p.value --soft-idr-threshold 0.05 --plot &
# python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf zIDR
rm *merged.sorted.bam
rm *pseudoRep1.bam
rm *pseudoRep2.bam
rm *narrowPeak
rm *peaks.xls
rm *summits.bed
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep2-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep2-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep2-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep2-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep2-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep2-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep2-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep2-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep2-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep2-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep2-vs-rep3-IDR 11 1.301029996 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep2-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.pseudoreps.IDR 11 1.301029996 Inf OMP-GFP_ATAC.pseudoreps.IDR_0.05 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep1-vs-rep2-IDR 11 1.301029996 Inf OMP-GFP_ATAC.rep1-vs-rep2-IDR_0.05 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep1-vs-rep3-IDR 11 1.301029996 Inf OMP-GFP_ATAC.rep1-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep2-vs-rep3-IDR 11 1.301029996 Inf OMP-GFP_ATAC.rep2-vs-rep3-IDR_0.05 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep2-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep2-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep1-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep2-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.rep2-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep2-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep2-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep1-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep2-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.rep2-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep2-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep2-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep1-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep2-vs-rep3-IDR 11 1 Inf mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.rep2-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.pseudoreps.IDR 11 1 Inf OMP-GFP_ATAC.pseudoreps.IDR_0.10 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep1-vs-rep2-IDR 11 1 Inf OMP-GFP_ATAC.rep1-vs-rep2-IDR_0.10 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep1-vs-rep3-IDR 11 1 Inf OMP-GFP_ATAC.rep1-vs-rep3-IDR_0.10 &
python ~/code/extractLinesByValue.py OMP-GFP_ATAC.rep2-vs-rep3-IDR 11 1 Inf OMP-GFP_ATAC.rep2-vs-rep3-IDR_0.10 &
gzip *IDR_0.05
gzip *IDR_0.10
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep1-GSM7679950.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05-rep1.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep2-GSM7679953.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05-rep2.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC_rep3-GSM7679956.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_ATAC.pseudoreps.IDR_0.05-rep3.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep1-GSM7679949.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05-rep1.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep2-GSM7679952.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05-rep2.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC_rep3-GSM7679955.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_GFPpos_tdTompos_ATAC.pseudoreps.IDR_0.05-rep3.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep1-GSM7679948.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05-rep1.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep2-GSM7679951.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05-rep2.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05.gz 0 mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC_rep3-GSM7679954.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes mor28iCre-tdTom_OMPtTA-tetOP2_tdTompos_ATAC.pseudoreps.IDR_0.05-rep3.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py OMP-GFP_ATAC.pseudoreps.IDR_0.05.gz 0 OMP-GFP_ATAC_rep1-GSM7679975.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC.pseudoreps.IDR_0.05-rep1.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py OMP-GFP_ATAC.pseudoreps.IDR_0.05.gz 0 OMP-GFP_ATAC_rep2-GSM7679976.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC.pseudoreps.IDR_0.05-rep2.RPM -RPM -printSum -uniqueBAM &
python ~/code/bedRPKMfromBAM.py OMP-GFP_ATAC.pseudoreps.IDR_0.05.gz 0 OMP-GFP_ATAC_rep3-GSM7679977.2x36mers.mm10.unique.nochrM.dedup.bam ~/genomes/mm10/mm10.chrom.sizes OMP-GFP_ATAC.pseudoreps.IDR_0.05-rep3.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SLURM.py z 1 20000 12:00:00 akundaje,normal,owners,sfgf zBRP