python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4286-HFF_4hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4286-HFF_4hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4286-HFF_4hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4286-HFF_4hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4286-HFF_4hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4286-HFF_4hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4287-HFF_12hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4287-HFF_12hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4287-HFF_12hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4287-HFF_12hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4287-HFF_12hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4287-HFF_12hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4288-HFF_24hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4288-HFF_24hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4288-HFF_24hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4288-HFF_24hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4288-HFF_24hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4288-HFF_24hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4289-HFF_48hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4289-HFF_48hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4289-HFF_48hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4289-HFF_48hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4289-HFF_48hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4289-HFF_48hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4290-HFF_72hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4290-HFF_72hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4290-HFF_72hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4290-HFF_72hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4290-HFF_72hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4290-HFF_72hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4291-HFF_96hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4291-HFF_96hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4291-HFF_96hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4291-HFF_96hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4291-HFF_96hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4291-HFF_96hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4292-HFF_120hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4292-HFF_120hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4292-HFF_120hpi_noPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4292-HFF_120hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4292-HFF_120hpi_noPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4292-HFF_120hpi_noPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4293-HFF_72hpi_1hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4293-HFF_72hpi_1hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4293-HFF_72hpi_1hpiPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4293-HFF_72hpi_1hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4293-HFF_72hpi_1hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4293-HFF_72hpi_1hpiPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4294-HFF_72hpi_48hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4294-HFF_72hpi_48hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4294-HFF_72hpi_48hpiPFA_1_Input.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4294-HFF_72hpi_48hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4294-HFF_72hpi_48hpiPFA_1_Input.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4294-HFF_72hpi_48hpiPFA_1_Input.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4295-HFF_4hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4295-HFF_4hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4295-HFF_4hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4295-HFF_4hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4295-HFF_4hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4295-HFF_4hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4296-HFF_12hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4296-HFF_12hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4296-HFF_12hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4296-HFF_12hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4296-HFF_12hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4296-HFF_12hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4297-HFF_24hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4297-HFF_24hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4297-HFF_24hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4297-HFF_24hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4297-HFF_24hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4297-HFF_24hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4298-HFF_48hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4298-HFF_48hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4298-HFF_48hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4298-HFF_48hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4298-HFF_48hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4298-HFF_48hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4299-HFF_72hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4299-HFF_72hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4299-HFF_72hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4299-HFF_72hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4299-HFF_72hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4299-HFF_72hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4300-HFF_96hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4300-HFF_96hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4300-HFF_96hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4300-HFF_96hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4300-HFF_96hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4300-HFF_96hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4301-HFF_120hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4301-HFF_120hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4301-HFF_120hpi_noPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4301-HFF_120hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4301-HFF_120hpi_noPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4301-HFF_120hpi_noPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4302-HFF_72hpi_1hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4302-HFF_72hpi_1hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4302-HFF_72hpi_1hpiPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4302-HFF_72hpi_1hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4302-HFF_72hpi_1hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4302-HFF_72hpi_1hpiPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4303-HFF_72hpi_48hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4303-HFF_72hpi_48hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4303-HFF_72hpi_48hpiPFA_1_CTCF.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4303-HFF_72hpi_48hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4303-HFF_72hpi_48hpiPFA_1_CTCF.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4303-HFF_72hpi_48hpiPFA_1_CTCF.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4304-HFF_4hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4304-HFF_4hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4304-HFF_4hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4304-HFF_4hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4304-HFF_4hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4304-HFF_4hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4305-HFF_12hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4305-HFF_12hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4305-HFF_12hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4305-HFF_12hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4305-HFF_12hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4305-HFF_12hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4306-HFF_24hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4306-HFF_24hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4306-HFF_24hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4306-HFF_24hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4306-HFF_24hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4306-HFF_24hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4307-HFF_48hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4307-HFF_48hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4307-HFF_48hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4307-HFF_48hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4307-HFF_48hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4307-HFF_48hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4308-HFF_72hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4308-HFF_72hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4308-HFF_72hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4308-HFF_72hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4308-HFF_72hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4308-HFF_72hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4309-HFF_96hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4309-HFF_96hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4309-HFF_96hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4309-HFF_96hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4309-HFF_96hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4309-HFF_96hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4310-HFF_120hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4310-HFF_120hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4310-HFF_120hpi_noPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4310-HFF_120hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4310-HFF_120hpi_noPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4310-HFF_120hpi_noPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4311-HFF_72hpi_1hpiPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4312-HFF_72hpi_48hpiPFA_1_H3K27ac.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4313-HFF_4hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4313-HFF_4hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4313-HFF_4hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4313-HFF_4hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4313-HFF_4hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4313-HFF_4hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4314-HFF_12hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4314-HFF_12hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4314-HFF_12hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4314-HFF_12hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4314-HFF_12hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4314-HFF_12hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4315-HFF_24hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4315-HFF_24hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4315-HFF_24hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4315-HFF_24hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4315-HFF_24hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4315-HFF_24hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4316-HFF_48hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4316-HFF_48hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4316-HFF_48hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4316-HFF_48hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4316-HFF_48hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4316-HFF_48hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4317-HFF_72hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4317-HFF_72hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4317-HFF_72hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4317-HFF_72hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4317-HFF_72hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4317-HFF_72hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4318-HFF_96hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4318-HFF_96hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4318-HFF_96hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4318-HFF_96hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4318-HFF_96hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4318-HFF_96hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4319-HFF_120hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4319-HFF_120hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4319-HFF_120hpi_noPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4319-HFF_120hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4319-HFF_120hpi_noPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4319-HFF_120hpi_noPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4320-HFF_72hpi_1hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4320-HFF_72hpi_1hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4320-HFF_72hpi_1hpiPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4320-HFF_72hpi_1hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4320-HFF_72hpi_1hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4320-HFF_72hpi_1hpiPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4321-HFF_72hpi_48hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4321-HFF_72hpi_48hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4321-HFF_72hpi_48hpiPFA_1_4H8.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4321-HFF_72hpi_48hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4321-HFF_72hpi_48hpiPFA_1_4H8.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4321-HFF_72hpi_48hpiPFA_1_4H8.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4322-HFF_4hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4322-HFF_4hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4322-HFF_4hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4322-HFF_4hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4322-HFF_4hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4322-HFF_4hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4323-HFF_12hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4323-HFF_12hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4323-HFF_12hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4323-HFF_12hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4323-HFF_12hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4323-HFF_12hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4324-HFF_24hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4324-HFF_24hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4324-HFF_24hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4324-HFF_24hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4324-HFF_24hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4324-HFF_24hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4325-HFF_72hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4325-HFF_72hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4325-HFF_72hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4325-HFF_72hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4325-HFF_72hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4325-HFF_72hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4326-HFF_96hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4326-HFF_96hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4326-HFF_96hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4326-HFF_96hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4326-HFF_96hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4326-HFF_96hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4327-HFF_120hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4327-HFF_120hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4327-HFF_120hpi_noPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4327-HFF_120hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4327-HFF_120hpi_noPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4327-HFF_120hpi_noPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4328-HFF_72hpi_1hpiPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4329-HFF_72hpi_48hpiPFA_1_H3K4me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4330-HFF_4hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4330-HFF_4hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4330-HFF_4hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4330-HFF_4hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4330-HFF_4hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4330-HFF_4hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4331-HFF_12hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4331-HFF_12hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4331-HFF_12hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4331-HFF_12hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4331-HFF_12hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4331-HFF_12hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4332-HFF_24hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4332-HFF_24hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4332-HFF_24hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4332-HFF_24hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4332-HFF_24hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4332-HFF_24hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4333-HFF_48hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4333-HFF_48hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4333-HFF_48hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4333-HFF_48hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4333-HFF_48hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4333-HFF_48hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4334-HFF_72hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4334-HFF_72hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4334-HFF_72hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4334-HFF_72hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4334-HFF_72hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4334-HFF_72hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4335-HFF_96hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4335-HFF_96hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4335-HFF_96hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4335-HFF_96hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4335-HFF_96hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4335-HFF_96hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4336-HFF_120hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4336-HFF_120hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4336-HFF_120hpi_noPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4336-HFF_120hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4336-HFF_120hpi_noPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4336-HFF_120hpi_noPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4337-HFF_72hpi_1hpiPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4338-HFF_72hpi_48hpiPFA_1_H3K9me3.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4339-HFF_4hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4339-HFF_4hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4339-HFF_4hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4339-HFF_4hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4339-HFF_4hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4339-HFF_4hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4340-HFF_12hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4340-HFF_12hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4340-HFF_12hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4340-HFF_12hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4340-HFF_12hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4340-HFF_12hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4341-HFF_24hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4341-HFF_24hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4341-HFF_24hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4341-HFF_24hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4341-HFF_24hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4341-HFF_24hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4342-HFF_48hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4342-HFF_48hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4342-HFF_48hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4342-HFF_48hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4342-HFF_48hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4342-HFF_48hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4343-HFF_72hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4343-HFF_72hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4343-HFF_72hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4343-HFF_72hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4343-HFF_72hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4343-HFF_72hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4344-HFF_96hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4344-HFF_96hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4344-HFF_96hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4344-HFF_96hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4344-HFF_96hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4344-HFF_96hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4345-HFF_120hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4345-HFF_120hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4345-HFF_120hpi_noPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4345-HFF_120hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4345-HFF_120hpi_noPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4345-HFF_120hpi_noPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4346-HFF_72hpi_1hpiPFA_1_H3K4me1.merlin.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/hg20/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.hg38-male.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end1.fastq.gz L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.250820_NB551514_0339_AHHLC5BGYX.end2.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/Viruses/HCMV/bowtie-indexes/merlin -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/bowtie-indexes/merlin.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L4347-HFF_72hpi_48hpiPFA_1_H3K4me1.merlin.2x36mers.unique