zcat HepG2-AGGF1-human-ENCSR543TPH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1-human-ENCSR543TPH-rep1.1x36mers.chrM.unique
zcat HepG2-AGGF1-human-ENCSR543TPH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1-human-ENCSR543TPH-rep2.1x36mers.chrM.unique
zcat HepG2-AGGF1_eCLIP_mock_input-human-ENCSR182AEG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1_eCLIP_mock_input-human-ENCSR182AEG-rep1.1x36mers.chrM.unique
zcat HepG2-BCCIP-human-ENCSR485QCG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP-human-ENCSR485QCG-rep1.1x36mers.chrM.unique
zcat HepG2-BCCIP-human-ENCSR485QCG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP-human-ENCSR485QCG-rep2.1x36mers.chrM.unique
zcat HepG2-BCCIP_eCLIP_mock_input-human-ENCSR655BRZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP_eCLIP_mock_input-human-ENCSR655BRZ-rep1.1x36mers.chrM.unique
zcat HepG2-BUD13-human-ENCSR830BSQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13-human-ENCSR830BSQ-rep1.1x36mers.chrM.unique
zcat HepG2-BUD13-human-ENCSR830BSQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13-human-ENCSR830BSQ-rep2.1x36mers.chrM.unique
zcat HepG2-BUD13_eCLIP_mock_input-human-ENCSR777PDA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13_eCLIP_mock_input-human-ENCSR777PDA-rep1.1x36mers.chrM.unique
zcat HepG2-CDC40-human-ENCSR815VVI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40-human-ENCSR815VVI-rep1.1x36mers.chrM.unique
zcat HepG2-CDC40-human-ENCSR815VVI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40-human-ENCSR815VVI-rep2.1x36mers.chrM.unique
zcat HepG2-CDC40_eCLIP_mock_input-human-ENCSR828ALT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40_eCLIP_mock_input-human-ENCSR828ALT-rep1.1x36mers.chrM.unique
zcat HepG2-CSTF2-human-ENCSR384MWO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2-human-ENCSR384MWO-rep1.1x36mers.chrM.unique
zcat HepG2-CSTF2-human-ENCSR384MWO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2-human-ENCSR384MWO-rep2.1x36mers.chrM.unique
zcat HepG2-CSTF2T-human-ENCSR919HSE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T-human-ENCSR919HSE-rep1.1x36mers.chrM.unique
zcat HepG2-CSTF2T-human-ENCSR919HSE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T-human-ENCSR919HSE-rep2.1x36mers.chrM.unique
zcat HepG2-CSTF2T_eCLIP_mock_input-human-ENCSR391GLS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T_eCLIP_mock_input-human-ENCSR391GLS-rep1.1x36mers.chrM.unique
zcat HepG2-CSTF2_eCLIP_mock_input-human-ENCSR309GHK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2_eCLIP_mock_input-human-ENCSR309GHK-rep1.1x36mers.chrM.unique
zcat HepG2-DDX20_eCLIP_mock_input-human-ENCSR240ZFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX20_eCLIP_mock_input-human-ENCSR240ZFU-rep1.1x36mers.chrM.unique
zcat HepG2-DDX3X-human-ENCSR648LAH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X-human-ENCSR648LAH-rep1.1x36mers.chrM.unique
zcat HepG2-DDX3X-human-ENCSR648LAH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X-human-ENCSR648LAH-rep2.1x36mers.chrM.unique
zcat HepG2-DDX3X_eCLIP_mock_input-human-ENCSR090VXV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X_eCLIP_mock_input-human-ENCSR090VXV-rep1.1x36mers.chrM.unique
zcat HepG2-DDX55-human-ENCSR845VGB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55-human-ENCSR845VGB-rep1.1x36mers.chrM.unique
zcat HepG2-DDX55-human-ENCSR845VGB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55-human-ENCSR845VGB-rep2.1x36mers.chrM.unique
zcat HepG2-DDX55_eCLIP_mock_input-human-ENCSR454OFD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55_eCLIP_mock_input-human-ENCSR454OFD-rep1.1x36mers.chrM.unique
zcat HepG2-DDX59-human-ENCSR214BZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59-human-ENCSR214BZA-rep1.1x36mers.chrM.unique
zcat HepG2-DDX59-human-ENCSR214BZA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59-human-ENCSR214BZA-rep2.1x36mers.chrM.unique
zcat HepG2-DDX59_eCLIP_mock_input-human-ENCSR334OMC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59_eCLIP_mock_input-human-ENCSR334OMC-rep1.1x36mers.chrM.unique
zcat HepG2-DDX6-human-ENCSR141OIM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6-human-ENCSR141OIM-rep1.1x36mers.chrM.unique
zcat HepG2-DDX6-human-ENCSR141OIM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6-human-ENCSR141OIM-rep2.1x36mers.chrM.unique
zcat HepG2-DDX6_eCLIP_mock_input-human-ENCSR099KAK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6_eCLIP_mock_input-human-ENCSR099KAK-rep1.1x36mers.chrM.unique
zcat HepG2-DGCR8-human-ENCSR061SZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8-human-ENCSR061SZV-rep1.1x36mers.chrM.unique
zcat HepG2-DGCR8-human-ENCSR061SZV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8-human-ENCSR061SZV-rep2.1x36mers.chrM.unique
zcat HepG2-DGCR8_eCLIP_mock_input-human-ENCSR298SAD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8_eCLIP_mock_input-human-ENCSR298SAD-rep1.1x36mers.chrM.unique
zcat HepG2-DHX30-human-ENCSR565DGW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30-human-ENCSR565DGW-rep1.1x36mers.chrM.unique
zcat HepG2-DHX30-human-ENCSR565DGW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30-human-ENCSR565DGW-rep2.1x36mers.chrM.unique
zcat HepG2-DHX30_eCLIP_mock_input-human-ENCSR151MPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30_eCLIP_mock_input-human-ENCSR151MPZ-rep1.1x36mers.chrM.unique
zcat HepG2-DKC1-human-ENCSR301TFY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1-human-ENCSR301TFY-rep1.1x36mers.chrM.unique
zcat HepG2-DKC1-human-ENCSR301TFY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1-human-ENCSR301TFY-rep2.1x36mers.chrM.unique
zcat HepG2-DKC1_eCLIP_mock_input-human-ENCSR197LHH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1_eCLIP_mock_input-human-ENCSR197LHH-rep1.1x36mers.chrM.unique
zcat HepG2-DROSHA-human-ENCSR834YLD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA-human-ENCSR834YLD-rep1.1x36mers.chrM.unique
zcat HepG2-DROSHA-human-ENCSR834YLD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA-human-ENCSR834YLD-rep2.1x36mers.chrM.unique
zcat HepG2-DROSHA_eCLIP_mock_input-human-ENCSR785VKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA_eCLIP_mock_input-human-ENCSR785VKF-rep1.1x36mers.chrM.unique
zcat HepG2-EFTUD2-human-ENCSR527DXF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2-human-ENCSR527DXF-rep1.1x36mers.chrM.unique
zcat HepG2-EFTUD2-human-ENCSR527DXF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2-human-ENCSR527DXF-rep2.1x36mers.chrM.unique
zcat HepG2-EFTUD2_eCLIP_mock_input-human-ENCSR878HWU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2_eCLIP_mock_input-human-ENCSR878HWU-rep1.1x36mers.chrM.unique
zcat HepG2-EIF3D-human-ENCSR041NUV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D-human-ENCSR041NUV-rep1.1x36mers.chrM.unique
zcat HepG2-EIF3D-human-ENCSR041NUV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D-human-ENCSR041NUV-rep2.1x36mers.chrM.unique
zcat HepG2-EIF3D_eCLIP_mock_input-human-ENCSR755PSW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D_eCLIP_mock_input-human-ENCSR755PSW-rep1.1x36mers.chrM.unique
zcat HepG2-EIF3H-human-ENCSR916XIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H-human-ENCSR916XIV-rep1.1x36mers.chrM.unique
zcat HepG2-EIF3H-human-ENCSR916XIV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H-human-ENCSR916XIV-rep2.1x36mers.chrM.unique
zcat HepG2-EIF3H_eCLIP_mock_input-human-ENCSR756NPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H_eCLIP_mock_input-human-ENCSR756NPZ-rep1.1x36mers.chrM.unique
zcat HepG2-FAM120A-human-ENCSR987NYS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A-human-ENCSR987NYS-rep1.1x36mers.chrM.unique
zcat HepG2-FAM120A-human-ENCSR987NYS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A-human-ENCSR987NYS-rep2.1x36mers.chrM.unique
zcat HepG2-FAM120A_eCLIP_mock_input-human-ENCSR839KAX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A_eCLIP_mock_input-human-ENCSR839KAX-rep1.1x36mers.chrM.unique
zcat HepG2-FASTKD2-human-ENCSR023UHL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2-human-ENCSR023UHL-rep1.1x36mers.chrM.unique
zcat HepG2-FASTKD2-human-ENCSR023UHL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2-human-ENCSR023UHL-rep2.1x36mers.chrM.unique
zcat HepG2-FASTKD2_eCLIP_mock_input-human-ENCSR671FKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2_eCLIP_mock_input-human-ENCSR671FKF-rep1.1x36mers.chrM.unique
zcat HepG2-FKBP4-human-ENCSR018ZUE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4-human-ENCSR018ZUE-rep1.1x36mers.chrM.unique
zcat HepG2-FKBP4-human-ENCSR018ZUE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4-human-ENCSR018ZUE-rep2.1x36mers.chrM.unique
zcat HepG2-FKBP4_eCLIP_mock_input-human-ENCSR704LTK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4_eCLIP_mock_input-human-ENCSR704LTK-rep1.1x36mers.chrM.unique
zcat HepG2-FUBP3-human-ENCSR486YGP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3-human-ENCSR486YGP-rep1.1x36mers.chrM.unique
zcat HepG2-FUBP3-human-ENCSR486YGP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3-human-ENCSR486YGP-rep2.1x36mers.chrM.unique
zcat HepG2-FUBP3_eCLIP_mock_input-human-ENCSR056RZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3_eCLIP_mock_input-human-ENCSR056RZV-rep1.1x36mers.chrM.unique
zcat HepG2-GRSF1-human-ENCSR668MJX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1-human-ENCSR668MJX-rep1.1x36mers.chrM.unique
zcat HepG2-GRSF1-human-ENCSR668MJX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1-human-ENCSR668MJX-rep2.1x36mers.chrM.unique
zcat HepG2-GRSF1_eCLIP_mock_input-human-ENCSR638YHN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1_eCLIP_mock_input-human-ENCSR638YHN-rep1.1x36mers.chrM.unique
zcat HepG2-GRWD1-human-ENCSR893NWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1-human-ENCSR893NWB-rep1.1x36mers.chrM.unique
zcat HepG2-GRWD1-human-ENCSR893NWB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1-human-ENCSR893NWB-rep2.1x36mers.chrM.unique
zcat HepG2-GRWD1_eCLIP_mock_input-human-ENCSR835ZOK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1_eCLIP_mock_input-human-ENCSR835ZOK-rep1.1x36mers.chrM.unique
zcat HepG2-GTF2F1-human-ENCSR265ZIS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1-human-ENCSR265ZIS-rep1.1x36mers.chrM.unique
zcat HepG2-GTF2F1-human-ENCSR265ZIS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1-human-ENCSR265ZIS-rep2.1x36mers.chrM.unique
zcat HepG2-GTF2F1_eCLIP_mock_input-human-ENCSR451HMR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1_eCLIP_mock_input-human-ENCSR451HMR-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPA1-human-ENCSR769UEW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1-human-ENCSR769UEW-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPA1-human-ENCSR769UEW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1-human-ENCSR769UEW-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPA1_eCLIP_mock_input-human-ENCSR110XNS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1_eCLIP_mock_input-human-ENCSR110XNS-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPC-human-ENCSR550DVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC-human-ENCSR550DVK-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPC-human-ENCSR550DVK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC-human-ENCSR550DVK-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPC_eCLIP_mock_input-human-ENCSR497ANA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC_eCLIP_mock_input-human-ENCSR497ANA-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPK-human-ENCSR828ZID-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK-human-ENCSR828ZID-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPK-human-ENCSR828ZID-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK-human-ENCSR828ZID-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPK_eCLIP_mock_input-human-ENCSR354KAS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK_eCLIP_mock_input-human-ENCSR354KAS-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPL-human-ENCSR724RDN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL-human-ENCSR724RDN-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPL-human-ENCSR724RDN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL-human-ENCSR724RDN-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPL_eCLIP_mock_input-human-ENCSR513UTE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL_eCLIP_mock_input-human-ENCSR513UTE-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPM-human-ENCSR267UCX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM-human-ENCSR267UCX-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPM-human-ENCSR267UCX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM-human-ENCSR267UCX-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPM_eCLIP_mock_input-human-ENCSR459ONR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM_eCLIP_mock_input-human-ENCSR459ONR-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPU-human-ENCSR240MVJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU-human-ENCSR240MVJ-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPU-human-ENCSR240MVJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU-human-ENCSR240MVJ-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPUL1-human-ENCSR755TJC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1-human-ENCSR755TJC-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPUL1-human-ENCSR755TJC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1-human-ENCSR755TJC-rep2.1x36mers.chrM.unique
zcat HepG2-HNRNPUL1_eCLIP_mock_input-human-ENCSR643JMB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1_eCLIP_mock_input-human-ENCSR643JMB-rep1.1x36mers.chrM.unique
zcat HepG2-HNRNPU_eCLIP_mock_input-human-ENCSR614VYQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU_eCLIP_mock_input-human-ENCSR614VYQ-rep1.1x36mers.chrM.unique
zcat HepG2-IGF2BP1-human-ENCSR744GEU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1-human-ENCSR744GEU-rep1.1x36mers.chrM.unique
zcat HepG2-IGF2BP1-human-ENCSR744GEU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1-human-ENCSR744GEU-rep2.1x36mers.chrM.unique
zcat HepG2-IGF2BP1_eCLIP_mock_input-human-ENCSR205ZCE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1_eCLIP_mock_input-human-ENCSR205ZCE-rep1.1x36mers.chrM.unique
zcat HepG2-IGF2BP3-human-ENCSR993OLA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3-human-ENCSR993OLA-rep1.1x36mers.chrM.unique
zcat HepG2-IGF2BP3-human-ENCSR993OLA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3-human-ENCSR993OLA-rep2.1x36mers.chrM.unique
zcat HepG2-IGF2BP3_eCLIP_mock_input-human-ENCSR077KVG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3_eCLIP_mock_input-human-ENCSR077KVG-rep1.1x36mers.chrM.unique
zcat HepG2-ILF3-human-ENCSR786TSC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3-human-ENCSR786TSC-rep1.1x36mers.chrM.unique
zcat HepG2-ILF3-human-ENCSR786TSC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3-human-ENCSR786TSC-rep2.1x36mers.chrM.unique
zcat HepG2-ILF3_eCLIP_mock_input-human-ENCSR080OLK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3_eCLIP_mock_input-human-ENCSR080OLK-rep1.1x36mers.chrM.unique
zcat HepG2-LARP4-human-ENCSR805SRN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4-human-ENCSR805SRN-rep1.1x36mers.chrM.unique
zcat HepG2-LARP4-human-ENCSR805SRN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4-human-ENCSR805SRN-rep2.1x36mers.chrM.unique
zcat HepG2-LARP4_eCLIP_mock_input-human-ENCSR192PUP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4_eCLIP_mock_input-human-ENCSR192PUP-rep1.1x36mers.chrM.unique
zcat HepG2-LARP7-human-ENCSR961OKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7-human-ENCSR961OKA-rep1.1x36mers.chrM.unique
zcat HepG2-LARP7-human-ENCSR961OKA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7-human-ENCSR961OKA-rep2.1x36mers.chrM.unique
zcat HepG2-LARP7_eCLIP_mock_input-human-ENCSR095SIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7_eCLIP_mock_input-human-ENCSR095SIV-rep1.1x36mers.chrM.unique
zcat HepG2-LIN28B-human-ENCSR861GYE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B-human-ENCSR861GYE-rep1.1x36mers.chrM.unique
zcat HepG2-LIN28B-human-ENCSR861GYE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B-human-ENCSR861GYE-rep2.1x36mers.chrM.unique
zcat HepG2-LIN28B_eCLIP_mock_input-human-ENCSR746ZSV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B_eCLIP_mock_input-human-ENCSR746ZSV-rep1.1x36mers.chrM.unique
zcat HepG2-LSM11-human-ENCSR135VMS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11-human-ENCSR135VMS-rep1.1x36mers.chrM.unique
zcat HepG2-LSM11-human-ENCSR135VMS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11-human-ENCSR135VMS-rep2.1x36mers.chrM.unique
zcat HepG2-LSM11_eCLIP_mock_input-human-ENCSR114XBO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11_eCLIP_mock_input-human-ENCSR114XBO-rep1.1x36mers.chrM.unique
zcat HepG2-MATR3-human-ENCSR290VLT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3-human-ENCSR290VLT-rep1.1x36mers.chrM.unique
zcat HepG2-MATR3-human-ENCSR290VLT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3-human-ENCSR290VLT-rep2.1x36mers.chrM.unique
zcat HepG2-MATR3_eCLIP_mock_input-human-ENCSR438XYI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3_eCLIP_mock_input-human-ENCSR438XYI-rep1.1x36mers.chrM.unique
zcat HepG2-NCBP2-human-ENCSR018RVZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2-human-ENCSR018RVZ-rep1.1x36mers.chrM.unique
zcat HepG2-NCBP2-human-ENCSR018RVZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2-human-ENCSR018RVZ-rep2.1x36mers.chrM.unique
zcat HepG2-NCBP2_eCLIP_mock_input-human-ENCSR257OYO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2_eCLIP_mock_input-human-ENCSR257OYO-rep1.1x36mers.chrM.unique
zcat HepG2-NKRF-human-ENCSR277DEO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF-human-ENCSR277DEO-rep1.1x36mers.chrM.unique
zcat HepG2-NKRF-human-ENCSR277DEO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF-human-ENCSR277DEO-rep2.1x36mers.chrM.unique
zcat HepG2-NKRF_eCLIP_mock_input-human-ENCSR479XOI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF_eCLIP_mock_input-human-ENCSR479XOI-rep1.1x36mers.chrM.unique
zcat HepG2-NOL12-human-ENCSR820DQJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12-human-ENCSR820DQJ-rep1.1x36mers.chrM.unique
zcat HepG2-NOL12-human-ENCSR820DQJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12-human-ENCSR820DQJ-rep2.1x36mers.chrM.unique
zcat HepG2-NOL12_eCLIP_mock_input-human-ENCSR709ABG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12_eCLIP_mock_input-human-ENCSR709ABG-rep1.1x36mers.chrM.unique
zcat HepG2-NOLC1-human-ENCSR194HZU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1-human-ENCSR194HZU-rep1.1x36mers.chrM.unique
zcat HepG2-NOLC1-human-ENCSR194HZU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1-human-ENCSR194HZU-rep2.1x36mers.chrM.unique
zcat HepG2-NOLC1_eCLIP_mock_input-human-ENCSR278BZH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1_eCLIP_mock_input-human-ENCSR278BZH-rep1.1x36mers.chrM.unique
zcat HepG2-PCBP2-human-ENCSR339FUY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2-human-ENCSR339FUY-rep1.1x36mers.chrM.unique
zcat HepG2-PCBP2-human-ENCSR339FUY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2-human-ENCSR339FUY-rep2.1x36mers.chrM.unique
zcat HepG2-PCBP2_eCLIP_mock_input-human-ENCSR115GAA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2_eCLIP_mock_input-human-ENCSR115GAA-rep1.1x36mers.chrM.unique
zcat HepG2-POLR2G-human-ENCSR820WHR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G-human-ENCSR820WHR-rep1.1x36mers.chrM.unique
zcat HepG2-POLR2G-human-ENCSR820WHR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G-human-ENCSR820WHR-rep2.1x36mers.chrM.unique
zcat HepG2-POLR2G_eCLIP_mock_input-human-ENCSR129SCO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G_eCLIP_mock_input-human-ENCSR129SCO-rep1.1x36mers.chrM.unique
zcat HepG2-PPIG-human-ENCSR097NEE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG-human-ENCSR097NEE-rep1.1x36mers.chrM.unique
zcat HepG2-PPIG-human-ENCSR097NEE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG-human-ENCSR097NEE-rep2.1x36mers.chrM.unique
zcat HepG2-PPIG_eCLIP_mock_input-human-ENCSR445LJH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG_eCLIP_mock_input-human-ENCSR445LJH-rep1.1x36mers.chrM.unique
zcat HepG2-PRPF8-human-ENCSR121NVA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8-human-ENCSR121NVA-rep1.1x36mers.chrM.unique
zcat HepG2-PRPF8-human-ENCSR121NVA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8-human-ENCSR121NVA-rep2.1x36mers.chrM.unique
zcat HepG2-PRPF8_eCLIP_mock_input-human-ENCSR565KBR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8_eCLIP_mock_input-human-ENCSR565KBR-rep1.1x36mers.chrM.unique
zcat HepG2-PTBP1-human-ENCSR384KAN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1-human-ENCSR384KAN-rep1.1x36mers.chrM.unique
zcat HepG2-PTBP1-human-ENCSR384KAN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1-human-ENCSR384KAN-rep2.1x36mers.chrM.unique
zcat HepG2-PTBP1_eCLIP_mock_input-human-ENCSR438NCK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1_eCLIP_mock_input-human-ENCSR438NCK-rep1.1x36mers.chrM.unique
zcat HepG2-QKI-human-ENCSR570WLM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI-human-ENCSR570WLM-rep1.1x36mers.chrM.unique
zcat HepG2-QKI-human-ENCSR570WLM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI-human-ENCSR570WLM-rep2.1x36mers.chrM.unique
zcat HepG2-QKI_eCLIP_mock_input-human-ENCSR130TOJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI_eCLIP_mock_input-human-ENCSR130TOJ-rep1.1x36mers.chrM.unique
zcat HepG2-RBFOX2-human-ENCSR987FTF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2-human-ENCSR987FTF-rep1.1x36mers.chrM.unique
zcat HepG2-RBFOX2-human-ENCSR987FTF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2-human-ENCSR987FTF-rep2.1x36mers.chrM.unique
zcat HepG2-RBFOX2_eCLIP_mock_input-human-ENCSR799EKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2_eCLIP_mock_input-human-ENCSR799EKA-rep1.1x36mers.chrM.unique
zcat HepG2-RBM15-human-ENCSR754NDA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15-human-ENCSR754NDA-rep1.1x36mers.chrM.unique
zcat HepG2-RBM15-human-ENCSR754NDA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15-human-ENCSR754NDA-rep2.1x36mers.chrM.unique
zcat HepG2-RBM15_eCLIP_mock_input-human-ENCSR317PWQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15_eCLIP_mock_input-human-ENCSR317PWQ-rep1.1x36mers.chrM.unique
zcat HepG2-RBM22-human-ENCSR456JJQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22-human-ENCSR456JJQ-rep1.1x36mers.chrM.unique
zcat HepG2-RBM22-human-ENCSR456JJQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22-human-ENCSR456JJQ-rep2.1x36mers.chrM.unique
zcat HepG2-RBM22_eCLIP_mock_input-human-ENCSR775UPS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22_eCLIP_mock_input-human-ENCSR775UPS-rep1.1x36mers.chrM.unique
zcat HepG2-RBM5-human-ENCSR489ABS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5-human-ENCSR489ABS-rep1.1x36mers.chrM.unique
zcat HepG2-RBM5-human-ENCSR489ABS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5-human-ENCSR489ABS-rep2.1x36mers.chrM.unique
zcat HepG2-RBM5_eCLIP_mock_input-human-ENCSR414RME-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5_eCLIP_mock_input-human-ENCSR414RME-rep1.1x36mers.chrM.unique
zcat HepG2-RPL23A_eCLIP_mock_input-human-ENCSR224ECB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPL23A_eCLIP_mock_input-human-ENCSR224ECB-rep1.1x36mers.chrM.unique
zcat HepG2-RPS3-human-ENCSR766FAC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3-human-ENCSR766FAC-rep1.1x36mers.chrM.unique
zcat HepG2-RPS3-human-ENCSR766FAC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3-human-ENCSR766FAC-rep2.1x36mers.chrM.unique
zcat HepG2-RPS3_eCLIP_mock_input-human-ENCSR745BIL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3_eCLIP_mock_input-human-ENCSR745BIL-rep1.1x36mers.chrM.unique
zcat HepG2-RPS5_eCLIP_mock_input-human-ENCSR828MEJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS5_eCLIP_mock_input-human-ENCSR828MEJ-rep1.1x36mers.chrM.unique
zcat HepG2-SF3A3-human-ENCSR331MIC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3-human-ENCSR331MIC-rep1.1x36mers.chrM.unique
zcat HepG2-SF3A3-human-ENCSR331MIC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3-human-ENCSR331MIC-rep2.1x36mers.chrM.unique
zcat HepG2-SF3A3_eCLIP_mock_input-human-ENCSR859PUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3_eCLIP_mock_input-human-ENCSR859PUB-rep1.1x36mers.chrM.unique
zcat HepG2-SF3B4-human-ENCSR279UJF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4-human-ENCSR279UJF-rep1.1x36mers.chrM.unique
zcat HepG2-SF3B4-human-ENCSR279UJF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4-human-ENCSR279UJF-rep2.1x36mers.chrM.unique
zcat HepG2-SF3B4_eCLIP_mock_input-human-ENCSR886YYD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4_eCLIP_mock_input-human-ENCSR886YYD-rep1.1x36mers.chrM.unique
zcat HepG2-SFPQ-human-ENCSR965DLL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ-human-ENCSR965DLL-rep1.1x36mers.chrM.unique
zcat HepG2-SFPQ-human-ENCSR965DLL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ-human-ENCSR965DLL-rep2.1x36mers.chrM.unique
zcat HepG2-SFPQ_eCLIP_mock_input-human-ENCSR506EIW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ_eCLIP_mock_input-human-ENCSR506EIW-rep1.1x36mers.chrM.unique
zcat HepG2-SLTM-human-ENCSR351PVI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM-human-ENCSR351PVI-rep1.1x36mers.chrM.unique
zcat HepG2-SLTM-human-ENCSR351PVI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM-human-ENCSR351PVI-rep2.1x36mers.chrM.unique
zcat HepG2-SLTM_eCLIP_mock_input-human-ENCSR670UPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM_eCLIP_mock_input-human-ENCSR670UPZ-rep1.1x36mers.chrM.unique
zcat HepG2-SMNDC1-human-ENCSR373ODC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1-human-ENCSR373ODC-rep1.1x36mers.chrM.unique
zcat HepG2-SMNDC1-human-ENCSR373ODC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1-human-ENCSR373ODC-rep2.1x36mers.chrM.unique
zcat HepG2-SMNDC1_eCLIP_mock_input-human-ENCSR388VKV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1_eCLIP_mock_input-human-ENCSR388VKV-rep1.1x36mers.chrM.unique
zcat HepG2-SND1-human-ENCSR061EVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1-human-ENCSR061EVO-rep1.1x36mers.chrM.unique
zcat HepG2-SND1-human-ENCSR061EVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1-human-ENCSR061EVO-rep2.1x36mers.chrM.unique
zcat HepG2-SND1_eCLIP_mock_input-human-ENCSR167OYL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1_eCLIP_mock_input-human-ENCSR167OYL-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF1-human-ENCSR989VIY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1-human-ENCSR989VIY-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF1-human-ENCSR989VIY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1-human-ENCSR989VIY-rep2.1x36mers.chrM.unique
zcat HepG2-SRSF1_eCLIP_mock_input-human-ENCSR499ZCU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1_eCLIP_mock_input-human-ENCSR499ZCU-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF7-human-ENCSR513NDD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7-human-ENCSR513NDD-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF7-human-ENCSR513NDD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7-human-ENCSR513NDD-rep2.1x36mers.chrM.unique
zcat HepG2-SRSF7_eCLIP_mock_input-human-ENCSR629MQN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7_eCLIP_mock_input-human-ENCSR629MQN-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF9-human-ENCSR773KRC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9-human-ENCSR773KRC-rep1.1x36mers.chrM.unique
zcat HepG2-SRSF9-human-ENCSR773KRC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9-human-ENCSR773KRC-rep2.1x36mers.chrM.unique
zcat HepG2-SRSF9_eCLIP_mock_input-human-ENCSR060VZF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9_eCLIP_mock_input-human-ENCSR060VZF-rep1.1x36mers.chrM.unique
zcat HepG2-SUB1-human-ENCSR406OOZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1-human-ENCSR406OOZ-rep1.1x36mers.chrM.unique
zcat HepG2-SUB1-human-ENCSR406OOZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1-human-ENCSR406OOZ-rep2.1x36mers.chrM.unique
zcat HepG2-SUB1_eCLIP_mock_input-human-ENCSR641PRC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1_eCLIP_mock_input-human-ENCSR641PRC-rep1.1x36mers.chrM.unique
zcat HepG2-SUGP2-human-ENCSR506UPY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2-human-ENCSR506UPY-rep1.1x36mers.chrM.unique
zcat HepG2-SUGP2-human-ENCSR506UPY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2-human-ENCSR506UPY-rep2.1x36mers.chrM.unique
zcat HepG2-SUGP2_eCLIP_mock_input-human-ENCSR895TTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2_eCLIP_mock_input-human-ENCSR895TTM-rep1.1x36mers.chrM.unique
zcat HepG2-SUPV3L1-human-ENCSR580MFX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1-human-ENCSR580MFX-rep1.1x36mers.chrM.unique
zcat HepG2-SUPV3L1-human-ENCSR580MFX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1-human-ENCSR580MFX-rep2.1x36mers.chrM.unique
zcat HepG2-SUPV3L1_eCLIP_mock_input-human-ENCSR376KLZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1_eCLIP_mock_input-human-ENCSR376KLZ-rep1.1x36mers.chrM.unique
zcat HepG2-TAF15-human-ENCSR841EQA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15-human-ENCSR841EQA-rep1.1x36mers.chrM.unique
zcat HepG2-TAF15-human-ENCSR841EQA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15-human-ENCSR841EQA-rep2.1x36mers.chrM.unique
zcat HepG2-TAF15_eCLIP_mock_input-human-ENCSR708TCY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15_eCLIP_mock_input-human-ENCSR708TCY-rep1.1x36mers.chrM.unique
zcat HepG2-TBRG4-human-ENCSR916SRV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4-human-ENCSR916SRV-rep1.1x36mers.chrM.unique
zcat HepG2-TBRG4-human-ENCSR916SRV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4-human-ENCSR916SRV-rep2.1x36mers.chrM.unique
zcat HepG2-TBRG4_eCLIP_mock_input-human-ENCSR081WUU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4_eCLIP_mock_input-human-ENCSR081WUU-rep1.1x36mers.chrM.unique
zcat HepG2-TIA1-human-ENCSR623VEQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1-human-ENCSR623VEQ-rep1.1x36mers.chrM.unique
zcat HepG2-TIA1-human-ENCSR623VEQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1-human-ENCSR623VEQ-rep2.1x36mers.chrM.unique
zcat HepG2-TIA1_eCLIP_mock_input-human-ENCSR333PZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1_eCLIP_mock_input-human-ENCSR333PZV-rep1.1x36mers.chrM.unique
zcat HepG2-TNRC6A_eCLIP_mock_input-human-ENCSR188OHK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TNRC6A_eCLIP_mock_input-human-ENCSR188OHK-rep1.1x36mers.chrM.unique
zcat HepG2-TRA2A-human-ENCSR314UMJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A-human-ENCSR314UMJ-rep1.1x36mers.chrM.unique
zcat HepG2-TRA2A-human-ENCSR314UMJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A-human-ENCSR314UMJ-rep2.1x36mers.chrM.unique
zcat HepG2-TRA2A_eCLIP_mock_input-human-ENCSR544CTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A_eCLIP_mock_input-human-ENCSR544CTM-rep1.1x36mers.chrM.unique
zcat HepG2-TROVE2-human-ENCSR993FMY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2-human-ENCSR993FMY-rep1.1x36mers.chrM.unique
zcat HepG2-TROVE2-human-ENCSR993FMY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2-human-ENCSR993FMY-rep2.1x36mers.chrM.unique
zcat HepG2-TROVE2_eCLIP_mock_input-human-ENCSR619LRH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2_eCLIP_mock_input-human-ENCSR619LRH-rep1.1x36mers.chrM.unique
zcat HepG2-U2AF1-human-ENCSR328LLU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1-human-ENCSR328LLU-rep1.1x36mers.chrM.unique
zcat HepG2-U2AF1-human-ENCSR328LLU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1-human-ENCSR328LLU-rep2.1x36mers.chrM.unique
zcat HepG2-U2AF1_eCLIP_mock_input-human-ENCSR941GJG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1_eCLIP_mock_input-human-ENCSR941GJG-rep1.1x36mers.chrM.unique
zcat HepG2-U2AF2-human-ENCSR202BFN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2-human-ENCSR202BFN-rep1.1x36mers.chrM.unique
zcat HepG2-U2AF2-human-ENCSR202BFN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2-human-ENCSR202BFN-rep2.1x36mers.chrM.unique
zcat HepG2-U2AF2_eCLIP_mock_input-human-ENCSR049GND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2_eCLIP_mock_input-human-ENCSR049GND-rep1.1x36mers.chrM.unique
zcat HepG2-UCHL5-human-ENCSR490IEE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5-human-ENCSR490IEE-rep1.1x36mers.chrM.unique
zcat HepG2-UCHL5-human-ENCSR490IEE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5-human-ENCSR490IEE-rep2.1x36mers.chrM.unique
zcat HepG2-UCHL5_eCLIP_mock_input-human-ENCSR161TFX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5_eCLIP_mock_input-human-ENCSR161TFX-rep1.1x36mers.chrM.unique
zcat HepG2-XPO5-human-ENCSR921SXC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5-human-ENCSR921SXC-rep1.1x36mers.chrM.unique
zcat HepG2-XPO5-human-ENCSR921SXC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5-human-ENCSR921SXC-rep2.1x36mers.chrM.unique
zcat HepG2-XPO5_eCLIP_mock_input-human-ENCSR583KVR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5_eCLIP_mock_input-human-ENCSR583KVR-rep1.1x36mers.chrM.unique
zcat HepG2-XRCC6-human-ENCSR571ROL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6-human-ENCSR571ROL-rep1.1x36mers.chrM.unique
zcat HepG2-XRCC6-human-ENCSR571ROL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6-human-ENCSR571ROL-rep2.1x36mers.chrM.unique
zcat HepG2-XRCC6_eCLIP_mock_input-human-ENCSR044NGV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6_eCLIP_mock_input-human-ENCSR044NGV-rep1.1x36mers.chrM.unique
zcat HepG2-XRN2-human-ENCSR655NZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2-human-ENCSR655NZA-rep1.1x36mers.chrM.unique
zcat HepG2-XRN2-human-ENCSR655NZA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2-human-ENCSR655NZA-rep2.1x36mers.chrM.unique
zcat HepG2-XRN2_eCLIP_mock_input-human-ENCSR247PDK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2_eCLIP_mock_input-human-ENCSR247PDK-rep1.1x36mers.chrM.unique
zcat HepG2-ZC3H11A-human-ENCSR907GUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A-human-ENCSR907GUB-rep1.1x36mers.chrM.unique
zcat HepG2-ZC3H11A-human-ENCSR907GUB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A-human-ENCSR907GUB-rep2.1x36mers.chrM.unique
zcat HepG2-ZC3H11A_eCLIP_mock_input-human-ENCSR098VKQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A_eCLIP_mock_input-human-ENCSR098VKQ-rep1.1x36mers.chrM.unique
zcat K562-AARS-human-ENCSR825SVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS-human-ENCSR825SVO-rep1.1x36mers.chrM.unique
zcat K562-AARS-human-ENCSR825SVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS-human-ENCSR825SVO-rep2.1x36mers.chrM.unique
zcat K562-AARS_eCLIP_mock_input-human-ENCSR696PRX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS_eCLIP_mock_input-human-ENCSR696PRX-rep1.1x36mers.chrM.unique
zcat K562-AGGF1-human-ENCSR725ARB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1-human-ENCSR725ARB-rep1.1x36mers.chrM.unique
zcat K562-AGGF1-human-ENCSR725ARB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1-human-ENCSR725ARB-rep2.1x36mers.chrM.unique
zcat K562-AGGF1_eCLIP_mock_input-human-ENCSR910LAN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1_eCLIP_mock_input-human-ENCSR910LAN-rep1.1x36mers.chrM.unique
zcat K562-AKAP8L-human-ENCSR206RXT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L-human-ENCSR206RXT-rep1.1x36mers.chrM.unique
zcat K562-AKAP8L-human-ENCSR206RXT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L-human-ENCSR206RXT-rep2.1x36mers.chrM.unique
zcat K562-AKAP8L_eCLIP_mock_input-human-ENCSR550SGC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L_eCLIP_mock_input-human-ENCSR550SGC-rep1.1x36mers.chrM.unique
zcat K562-BUD13-human-ENCSR663WES-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13-human-ENCSR663WES-rep1.1x36mers.chrM.unique
zcat K562-BUD13-human-ENCSR663WES-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13-human-ENCSR663WES-rep2.1x36mers.chrM.unique
zcat K562-BUD13_eCLIP_mock_input-human-ENCSR736LKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13_eCLIP_mock_input-human-ENCSR736LKF-rep1.1x36mers.chrM.unique
zcat K562-CPSF6-human-ENCSR532VUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6-human-ENCSR532VUB-rep1.1x36mers.chrM.unique
zcat K562-CPSF6-human-ENCSR532VUB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6-human-ENCSR532VUB-rep2.1x36mers.chrM.unique
zcat K562-CPSF6_eCLIP_mock_input-human-ENCSR249WNK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6_eCLIP_mock_input-human-ENCSR249WNK-rep1.1x36mers.chrM.unique
zcat K562-CSTF2T-human-ENCSR840DRD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T-human-ENCSR840DRD-rep1.1x36mers.chrM.unique
zcat K562-CSTF2T-human-ENCSR840DRD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T-human-ENCSR840DRD-rep2.1x36mers.chrM.unique
zcat K562-CSTF2T_eCLIP_mock_input-human-ENCSR722LZB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T_eCLIP_mock_input-human-ENCSR722LZB-rep1.1x36mers.chrM.unique
zcat K562-DDX24-human-ENCSR999WKT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24-human-ENCSR999WKT-rep1.1x36mers.chrM.unique
zcat K562-DDX24-human-ENCSR999WKT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24-human-ENCSR999WKT-rep2.1x36mers.chrM.unique
zcat K562-DDX24_eCLIP_mock_input-human-ENCSR195IWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24_eCLIP_mock_input-human-ENCSR195IWB-rep1.1x36mers.chrM.unique
zcat K562-DDX3X-human-ENCSR930BZL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X-human-ENCSR930BZL-rep1.1x36mers.chrM.unique
zcat K562-DDX3X-human-ENCSR930BZL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X-human-ENCSR930BZL-rep2.1x36mers.chrM.unique
zcat K562-DDX3X_eCLIP_mock_input-human-ENCSR028CRL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X_eCLIP_mock_input-human-ENCSR028CRL-rep1.1x36mers.chrM.unique
zcat K562-DDX42-human-ENCSR576SHT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42-human-ENCSR576SHT-rep1.1x36mers.chrM.unique
zcat K562-DDX42-human-ENCSR576SHT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42-human-ENCSR576SHT-rep2.1x36mers.chrM.unique
zcat K562-DDX42_eCLIP_mock_input-human-ENCSR200SAU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42_eCLIP_mock_input-human-ENCSR200SAU-rep1.1x36mers.chrM.unique
zcat K562-DDX55-human-ENCSR923NKN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55-human-ENCSR923NKN-rep1.1x36mers.chrM.unique
zcat K562-DDX55-human-ENCSR923NKN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55-human-ENCSR923NKN-rep2.1x36mers.chrM.unique
zcat K562-DDX55_eCLIP_mock_input-human-ENCSR180EJY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55_eCLIP_mock_input-human-ENCSR180EJY-rep1.1x36mers.chrM.unique
zcat K562-DDX6-human-ENCSR893EFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6-human-ENCSR893EFU-rep1.1x36mers.chrM.unique
zcat K562-DDX6-human-ENCSR893EFU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6-human-ENCSR893EFU-rep2.1x36mers.chrM.unique
zcat K562-DDX6_eCLIP_mock_input-human-ENCSR207DWI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6_eCLIP_mock_input-human-ENCSR207DWI-rep1.1x36mers.chrM.unique
zcat K562-DGCR8-human-ENCSR947JVR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8-human-ENCSR947JVR-rep1.1x36mers.chrM.unique
zcat K562-DGCR8-human-ENCSR947JVR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8-human-ENCSR947JVR-rep2.1x36mers.chrM.unique
zcat K562-DGCR8_eCLIP_mock_input-human-ENCSR616BTD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8_eCLIP_mock_input-human-ENCSR616BTD-rep1.1x36mers.chrM.unique
zcat K562-DHX30-human-ENCSR529GSJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30-human-ENCSR529GSJ-rep1.1x36mers.chrM.unique
zcat K562-DHX30-human-ENCSR529GSJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30-human-ENCSR529GSJ-rep2.1x36mers.chrM.unique
zcat K562-DHX30_eCLIP_mock_input-human-ENCSR224SND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30_eCLIP_mock_input-human-ENCSR224SND-rep1.1x36mers.chrM.unique
zcat K562-DROSHA-human-ENCSR653HQC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA-human-ENCSR653HQC-rep1.1x36mers.chrM.unique
zcat K562-DROSHA-human-ENCSR653HQC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA-human-ENCSR653HQC-rep2.1x36mers.chrM.unique
zcat K562-DROSHA_eCLIP_mock_input-human-ENCSR828NSY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA_eCLIP_mock_input-human-ENCSR828NSY-rep1.1x36mers.chrM.unique
zcat K562-EFTUD2-human-ENCSR844RVX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2-human-ENCSR844RVX-rep1.1x36mers.chrM.unique
zcat K562-EFTUD2-human-ENCSR844RVX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2-human-ENCSR844RVX-rep2.1x36mers.chrM.unique
zcat K562-EFTUD2_eCLIP_mock_input-human-ENCSR266UVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2_eCLIP_mock_input-human-ENCSR266UVO-rep1.1x36mers.chrM.unique
zcat K562-EIF4G2-human-ENCSR307YIW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2-human-ENCSR307YIW-rep1.1x36mers.chrM.unique
zcat K562-EIF4G2-human-ENCSR307YIW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2-human-ENCSR307YIW-rep2.1x36mers.chrM.unique
zcat K562-EIF4G2_eCLIP_mock_input-human-ENCSR651NUF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2_eCLIP_mock_input-human-ENCSR651NUF-rep1.1x36mers.chrM.unique
zcat K562-EWSR1-human-ENCSR887LPK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1-human-ENCSR887LPK-rep1.1x36mers.chrM.unique
zcat K562-EWSR1-human-ENCSR887LPK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1-human-ENCSR887LPK-rep2.1x36mers.chrM.unique
zcat K562-EWSR1_eCLIP_mock_input-human-ENCSR067UKU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1_eCLIP_mock_input-human-ENCSR067UKU-rep1.1x36mers.chrM.unique
zcat K562-EXOSC5-human-ENCSR013CTQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5-human-ENCSR013CTQ-rep1.1x36mers.chrM.unique
zcat K562-EXOSC5-human-ENCSR013CTQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5-human-ENCSR013CTQ-rep2.1x36mers.chrM.unique
zcat K562-EXOSC5_eCLIP_mock_input-human-ENCSR308RMD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5_eCLIP_mock_input-human-ENCSR308RMD-rep1.1x36mers.chrM.unique
zcat K562-FAM120A-human-ENCSR006OEQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A-human-ENCSR006OEQ-rep1.1x36mers.chrM.unique
zcat K562-FAM120A-human-ENCSR006OEQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A-human-ENCSR006OEQ-rep2.1x36mers.chrM.unique
zcat K562-FAM120A_eCLIP_mock_input-human-ENCSR811FFO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A_eCLIP_mock_input-human-ENCSR811FFO-rep1.1x36mers.chrM.unique
zcat K562-FASTKD2-human-ENCSR887FHF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2-human-ENCSR887FHF-rep1.1x36mers.chrM.unique
zcat K562-FASTKD2-human-ENCSR887FHF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2-human-ENCSR887FHF-rep2.1x36mers.chrM.unique
zcat K562-FASTKD2_eCLIP_mock_input-human-ENCSR119AFY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2_eCLIP_mock_input-human-ENCSR119AFY-rep1.1x36mers.chrM.unique
zcat K562-FMR1-human-ENCSR331VNX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1-human-ENCSR331VNX-rep1.1x36mers.chrM.unique
zcat K562-FMR1-human-ENCSR331VNX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1-human-ENCSR331VNX-rep2.1x36mers.chrM.unique
zcat K562-FMR1_eCLIP_mock_input-human-ENCSR735MBZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1_eCLIP_mock_input-human-ENCSR735MBZ-rep1.1x36mers.chrM.unique
zcat K562-FTO-human-ENCSR989SMC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO-human-ENCSR989SMC-rep1.1x36mers.chrM.unique
zcat K562-FTO-human-ENCSR989SMC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO-human-ENCSR989SMC-rep2.1x36mers.chrM.unique
zcat K562-FTO_eCLIP_mock_input-human-ENCSR575DKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO_eCLIP_mock_input-human-ENCSR575DKE-rep1.1x36mers.chrM.unique
zcat K562-FXR1-human-ENCSR774RFN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1-human-ENCSR774RFN-rep1.1x36mers.chrM.unique
zcat K562-FXR1-human-ENCSR774RFN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1-human-ENCSR774RFN-rep2.1x36mers.chrM.unique
zcat K562-FXR1_eCLIP_mock_input-human-ENCSR562BJW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1_eCLIP_mock_input-human-ENCSR562BJW-rep1.1x36mers.chrM.unique
zcat K562-FXR2-human-ENCSR224QWC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2-human-ENCSR224QWC-rep1.1x36mers.chrM.unique
zcat K562-FXR2-human-ENCSR224QWC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2-human-ENCSR224QWC-rep2.1x36mers.chrM.unique
zcat K562-FXR2_eCLIP_mock_input-human-ENCSR411IMJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2_eCLIP_mock_input-human-ENCSR411IMJ-rep1.1x36mers.chrM.unique
zcat K562-GEMIN5-human-ENCSR238CLX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5-human-ENCSR238CLX-rep1.1x36mers.chrM.unique
zcat K562-GEMIN5-human-ENCSR238CLX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5-human-ENCSR238CLX-rep2.1x36mers.chrM.unique
zcat K562-GEMIN5_eCLIP_mock_input-human-ENCSR347MVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5_eCLIP_mock_input-human-ENCSR347MVO-rep1.1x36mers.chrM.unique
zcat K562-GNL3-human-ENCSR301UQM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3-human-ENCSR301UQM-rep1.1x36mers.chrM.unique
zcat K562-GNL3-human-ENCSR301UQM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3-human-ENCSR301UQM-rep2.1x36mers.chrM.unique
zcat K562-GNL3_eCLIP_mock_input-human-ENCSR977GTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3_eCLIP_mock_input-human-ENCSR977GTT-rep1.1x36mers.chrM.unique
zcat K562-GPKOW-human-ENCSR647CLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW-human-ENCSR647CLF-rep1.1x36mers.chrM.unique
zcat K562-GPKOW-human-ENCSR647CLF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW-human-ENCSR647CLF-rep2.1x36mers.chrM.unique
zcat K562-GPKOW_eCLIP_mock_input-human-ENCSR393STP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW_eCLIP_mock_input-human-ENCSR393STP-rep1.1x36mers.chrM.unique
zcat K562-GTF2F1-human-ENCSR736AAG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1-human-ENCSR736AAG-rep1.1x36mers.chrM.unique
zcat K562-GTF2F1-human-ENCSR736AAG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1-human-ENCSR736AAG-rep2.1x36mers.chrM.unique
zcat K562-GTF2F1_eCLIP_mock_input-human-ENCSR157BRV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1_eCLIP_mock_input-human-ENCSR157BRV-rep1.1x36mers.chrM.unique
zcat K562-HLTF-human-ENCSR589YHM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF-human-ENCSR589YHM-rep1.1x36mers.chrM.unique
zcat K562-HLTF-human-ENCSR589YHM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF-human-ENCSR589YHM-rep2.1x36mers.chrM.unique
zcat K562-HLTF_eCLIP_mock_input-human-ENCSR502NKG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF_eCLIP_mock_input-human-ENCSR502NKG-rep1.1x36mers.chrM.unique
zcat K562-HNRNPA1-human-ENCSR154HRN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1-human-ENCSR154HRN-rep1.1x36mers.chrM.unique
zcat K562-HNRNPA1-human-ENCSR154HRN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1-human-ENCSR154HRN-rep2.1x36mers.chrM.unique
zcat K562-HNRNPA1_eCLIP_mock_input-human-ENCSR898ZCL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1_eCLIP_mock_input-human-ENCSR898ZCL-rep1.1x36mers.chrM.unique
zcat K562-HNRNPK-human-ENCSR268ETU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK-human-ENCSR268ETU-rep1.1x36mers.chrM.unique
zcat K562-HNRNPK-human-ENCSR268ETU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK-human-ENCSR268ETU-rep2.1x36mers.chrM.unique
zcat K562-HNRNPK_eCLIP_mock_input-human-ENCSR669DKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK_eCLIP_mock_input-human-ENCSR669DKA-rep1.1x36mers.chrM.unique
zcat K562-HNRNPL-human-ENCSR795CAI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL-human-ENCSR795CAI-rep1.1x36mers.chrM.unique
zcat K562-HNRNPL-human-ENCSR795CAI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL-human-ENCSR795CAI-rep2.1x36mers.chrM.unique
zcat K562-HNRNPL_eCLIP_mock_input-human-ENCSR299AAB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL_eCLIP_mock_input-human-ENCSR299AAB-rep1.1x36mers.chrM.unique
zcat K562-HNRNPM-human-ENCSR412NOW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM-human-ENCSR412NOW-rep1.1x36mers.chrM.unique
zcat K562-HNRNPM-human-ENCSR412NOW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM-human-ENCSR412NOW-rep2.1x36mers.chrM.unique
zcat K562-HNRNPM_eCLIP_mock_input-human-ENCSR212ILN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM_eCLIP_mock_input-human-ENCSR212ILN-rep1.1x36mers.chrM.unique
zcat K562-HNRNPU-human-ENCSR520BZQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU-human-ENCSR520BZQ-rep1.1x36mers.chrM.unique
zcat K562-HNRNPU-human-ENCSR520BZQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU-human-ENCSR520BZQ-rep2.1x36mers.chrM.unique
zcat K562-HNRNPUL1-human-ENCSR571VHI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1-human-ENCSR571VHI-rep1.1x36mers.chrM.unique
zcat K562-HNRNPUL1-human-ENCSR571VHI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1-human-ENCSR571VHI-rep2.1x36mers.chrM.unique
zcat K562-HNRNPUL1_eCLIP_mock_input-human-ENCSR482AWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1_eCLIP_mock_input-human-ENCSR482AWB-rep1.1x36mers.chrM.unique
zcat K562-HNRNPU_eCLIP_mock_input-human-ENCSR829SLO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU_eCLIP_mock_input-human-ENCSR829SLO-rep1.1x36mers.chrM.unique
zcat K562-IGF2BP1-human-ENCSR975KIR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1-human-ENCSR975KIR-rep1.1x36mers.chrM.unique
zcat K562-IGF2BP1-human-ENCSR975KIR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1-human-ENCSR975KIR-rep2.1x36mers.chrM.unique
zcat K562-IGF2BP1_eCLIP_mock_input-human-ENCSR125CLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1_eCLIP_mock_input-human-ENCSR125CLF-rep1.1x36mers.chrM.unique
zcat K562-IGF2BP2-human-ENCSR062NNB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2-human-ENCSR062NNB-rep1.1x36mers.chrM.unique
zcat K562-IGF2BP2-human-ENCSR062NNB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2-human-ENCSR062NNB-rep2.1x36mers.chrM.unique
zcat K562-IGF2BP2_eCLIP_mock_input-human-ENCSR387RGT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2_eCLIP_mock_input-human-ENCSR387RGT-rep1.1x36mers.chrM.unique
zcat K562-ILF3-human-ENCSR438KWZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3-human-ENCSR438KWZ-rep1.1x36mers.chrM.unique
zcat K562-ILF3-human-ENCSR438KWZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3-human-ENCSR438KWZ-rep2.1x36mers.chrM.unique
zcat K562-ILF3_eCLIP_mock_input-human-ENCSR760SFB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3_eCLIP_mock_input-human-ENCSR760SFB-rep1.1x36mers.chrM.unique
zcat K562-KHDRBS1-human-ENCSR628IDK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1-human-ENCSR628IDK-rep1.1x36mers.chrM.unique
zcat K562-KHDRBS1-human-ENCSR628IDK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1-human-ENCSR628IDK-rep2.1x36mers.chrM.unique
zcat K562-KHDRBS1_eCLIP_mock_input-human-ENCSR197NFH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1_eCLIP_mock_input-human-ENCSR197NFH-rep1.1x36mers.chrM.unique
zcat K562-KHSRP-human-ENCSR438GZQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP-human-ENCSR438GZQ-rep1.1x36mers.chrM.unique
zcat K562-KHSRP-human-ENCSR438GZQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP-human-ENCSR438GZQ-rep2.1x36mers.chrM.unique
zcat K562-KHSRP_eCLIP_mock_input-human-ENCSR305IPT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP_eCLIP_mock_input-human-ENCSR305IPT-rep1.1x36mers.chrM.unique
zcat K562-LARP4-human-ENCSR888YTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4-human-ENCSR888YTT-rep1.1x36mers.chrM.unique
zcat K562-LARP4-human-ENCSR888YTT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4-human-ENCSR888YTT-rep2.1x36mers.chrM.unique
zcat K562-LARP4_eCLIP_mock_input-human-ENCSR679NKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4_eCLIP_mock_input-human-ENCSR679NKE-rep1.1x36mers.chrM.unique
zcat K562-LARP7-human-ENCSR456KXI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7-human-ENCSR456KXI-rep1.1x36mers.chrM.unique
zcat K562-LARP7-human-ENCSR456KXI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7-human-ENCSR456KXI-rep2.1x36mers.chrM.unique
zcat K562-LARP7_eCLIP_mock_input-human-ENCSR863ZGZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7_eCLIP_mock_input-human-ENCSR863ZGZ-rep1.1x36mers.chrM.unique
zcat K562-LIN28B-human-ENCSR970NKP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B-human-ENCSR970NKP-rep1.1x36mers.chrM.unique
zcat K562-LIN28B-human-ENCSR970NKP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B-human-ENCSR970NKP-rep2.1x36mers.chrM.unique
zcat K562-LIN28B_eCLIP_mock_input-human-ENCSR399CBP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B_eCLIP_mock_input-human-ENCSR399CBP-rep1.1x36mers.chrM.unique
zcat K562-LSM11-human-ENCSR022BVV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11-human-ENCSR022BVV-rep1.1x36mers.chrM.unique
zcat K562-LSM11-human-ENCSR022BVV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11-human-ENCSR022BVV-rep2.1x36mers.chrM.unique
zcat K562-LSM11_eCLIP_mock_input-human-ENCSR952UOL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11_eCLIP_mock_input-human-ENCSR952UOL-rep1.1x36mers.chrM.unique
zcat K562-METAP2-human-ENCSR303OQD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2-human-ENCSR303OQD-rep1.1x36mers.chrM.unique
zcat K562-METAP2-human-ENCSR303OQD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2-human-ENCSR303OQD-rep2.1x36mers.chrM.unique
zcat K562-METAP2_eCLIP_mock_input-human-ENCSR750NTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2_eCLIP_mock_input-human-ENCSR750NTM-rep1.1x36mers.chrM.unique
zcat K562-MTPAP-human-ENCSR200DKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP-human-ENCSR200DKE-rep1.1x36mers.chrM.unique
zcat K562-MTPAP-human-ENCSR200DKE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP-human-ENCSR200DKE-rep2.1x36mers.chrM.unique
zcat K562-MTPAP_eCLIP_mock_input-human-ENCSR927XDB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP_eCLIP_mock_input-human-ENCSR927XDB-rep1.1x36mers.chrM.unique
zcat K562-NCBP2-human-ENCSR484LTQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2-human-ENCSR484LTQ-rep1.1x36mers.chrM.unique
zcat K562-NCBP2-human-ENCSR484LTQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2-human-ENCSR484LTQ-rep2.1x36mers.chrM.unique
zcat K562-NCBP2_eCLIP_mock_input-human-ENCSR921SHJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2_eCLIP_mock_input-human-ENCSR921SHJ-rep1.1x36mers.chrM.unique
zcat K562-NFX1_eCLIP_mock_input-human-ENCSR821ESG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NFX1_eCLIP_mock_input-human-ENCSR821ESG-rep1.1x36mers.chrM.unique
zcat K562-NOLC1-human-ENCSR001VAC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1-human-ENCSR001VAC-rep1.1x36mers.chrM.unique
zcat K562-NOLC1-human-ENCSR001VAC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1-human-ENCSR001VAC-rep2.1x36mers.chrM.unique
zcat K562-NOLC1_eCLIP_mock_input-human-ENCSR009CIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1_eCLIP_mock_input-human-ENCSR009CIV-rep1.1x36mers.chrM.unique
zcat K562-NONO-human-ENCSR861PAR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO-human-ENCSR861PAR-rep1.1x36mers.chrM.unique
zcat K562-NONO-human-ENCSR861PAR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO-human-ENCSR861PAR-rep2.1x36mers.chrM.unique
zcat K562-NONO__eCLIP_mock_input-human-ENCSR487EUV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO__eCLIP_mock_input-human-ENCSR487EUV-rep1.1x36mers.chrM.unique
zcat K562-NPM1-human-ENCSR867DSZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1-human-ENCSR867DSZ-rep1.1x36mers.chrM.unique
zcat K562-NPM1-human-ENCSR867DSZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1-human-ENCSR867DSZ-rep2.1x36mers.chrM.unique
zcat K562-NPM1_eCLIP_mock_input-human-ENCSR468ZQA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1_eCLIP_mock_input-human-ENCSR468ZQA-rep1.1x36mers.chrM.unique
zcat K562-NSUN2-human-ENCSR081JYH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2-human-ENCSR081JYH-rep1.1x36mers.chrM.unique
zcat K562-NSUN2-human-ENCSR081JYH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2-human-ENCSR081JYH-rep2.1x36mers.chrM.unique
zcat K562-NSUN2_eCLIP_mock_input-human-ENCSR595PFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2_eCLIP_mock_input-human-ENCSR595PFU-rep1.1x36mers.chrM.unique
zcat K562-POLR2G_eCLIP_mock_input-human-ENCSR585TQT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-POLR2G_eCLIP_mock_input-human-ENCSR585TQT-rep1.1x36mers.chrM.unique
zcat K562-PPIL4-human-ENCSR197INS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4-human-ENCSR197INS-rep1.1x36mers.chrM.unique
zcat K562-PPIL4-human-ENCSR197INS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4-human-ENCSR197INS-rep2.1x36mers.chrM.unique
zcat K562-PPIL4_eCLIP_mock_input-human-ENCSR346IHS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4_eCLIP_mock_input-human-ENCSR346IHS-rep1.1x36mers.chrM.unique
zcat K562-PRPF8-human-ENCSR534YOI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8-human-ENCSR534YOI-rep1.1x36mers.chrM.unique
zcat K562-PRPF8-human-ENCSR534YOI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8-human-ENCSR534YOI-rep2.1x36mers.chrM.unique
zcat K562-PRPF8_eCLIP_mock_input-human-ENCSR096SZE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8_eCLIP_mock_input-human-ENCSR096SZE-rep1.1x36mers.chrM.unique
zcat K562-PTBP1-human-ENCSR981WKN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1-human-ENCSR981WKN-rep1.1x36mers.chrM.unique
zcat K562-PTBP1-human-ENCSR981WKN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1-human-ENCSR981WKN-rep2.1x36mers.chrM.unique
zcat K562-PTBP1_eCLIP_mock_input-human-ENCSR445FZX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1_eCLIP_mock_input-human-ENCSR445FZX-rep1.1x36mers.chrM.unique
zcat K562-PUM2-human-ENCSR661ICQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2-human-ENCSR661ICQ-rep1.1x36mers.chrM.unique
zcat K562-PUM2-human-ENCSR661ICQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2-human-ENCSR661ICQ-rep2.1x36mers.chrM.unique
zcat K562-PUM2_eCLIP_mock_input-human-ENCSR439GXW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2_eCLIP_mock_input-human-ENCSR439GXW-rep1.1x36mers.chrM.unique
zcat K562-PUS1-human-ENCSR291XPT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1-human-ENCSR291XPT-rep1.1x36mers.chrM.unique
zcat K562-PUS1-human-ENCSR291XPT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1-human-ENCSR291XPT-rep2.1x36mers.chrM.unique
zcat K562-PUS1_eCLIP_mock_input-human-ENCSR869TOB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1_eCLIP_mock_input-human-ENCSR869TOB-rep1.1x36mers.chrM.unique
zcat K562-QKI-human-ENCSR366YOG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI-human-ENCSR366YOG-rep1.1x36mers.chrM.unique
zcat K562-QKI-human-ENCSR366YOG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI-human-ENCSR366YOG-rep2.1x36mers.chrM.unique
zcat K562-QKI_eCLIP_mock_input-human-ENCSR615AAW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI_eCLIP_mock_input-human-ENCSR615AAW-rep1.1x36mers.chrM.unique
zcat K562-RBFOX2-human-ENCSR756CKJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2-human-ENCSR756CKJ-rep1.1x36mers.chrM.unique
zcat K562-RBFOX2-human-ENCSR756CKJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2-human-ENCSR756CKJ-rep2.1x36mers.chrM.unique
zcat K562-RBFOX2_eCLIP_mock_input-human-ENCSR051IXX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2_eCLIP_mock_input-human-ENCSR051IXX-rep1.1x36mers.chrM.unique
zcat K562-RBM15-human-ENCSR196INN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15-human-ENCSR196INN-rep1.1x36mers.chrM.unique
zcat K562-RBM15-human-ENCSR196INN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15-human-ENCSR196INN-rep2.1x36mers.chrM.unique
zcat K562-RBM15_eCLIP_mock_input-human-ENCSR454EER-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15_eCLIP_mock_input-human-ENCSR454EER-rep1.1x36mers.chrM.unique
zcat K562-RBM22-human-ENCSR295OKT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22-human-ENCSR295OKT-rep1.1x36mers.chrM.unique
zcat K562-RBM22-human-ENCSR295OKT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22-human-ENCSR295OKT-rep2.1x36mers.chrM.unique
zcat K562-RBM22_eCLIP_mock_input-human-ENCSR344EGD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22_eCLIP_mock_input-human-ENCSR344EGD-rep1.1x36mers.chrM.unique
zcat K562-RPS11-human-ENCSR269AJF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11-human-ENCSR269AJF-rep1.1x36mers.chrM.unique
zcat K562-RPS11-human-ENCSR269AJF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11-human-ENCSR269AJF-rep2.1x36mers.chrM.unique
zcat K562-RPS11_eCLIP_mock_input-human-ENCSR881RJL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11_eCLIP_mock_input-human-ENCSR881RJL-rep1.1x36mers.chrM.unique
zcat K562-RPS24_eCLIP_mock_input-human-ENCSR567ZND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS24_eCLIP_mock_input-human-ENCSR567ZND-rep1.1x36mers.chrM.unique
zcat K562-RPS3-human-ENCSR120EAR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3-human-ENCSR120EAR-rep1.1x36mers.chrM.unique
zcat K562-RPS3-human-ENCSR120EAR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3-human-ENCSR120EAR-rep2.1x36mers.chrM.unique
zcat K562-RPS3_eCLIP_mock_input-human-ENCSR494JFR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3_eCLIP_mock_input-human-ENCSR494JFR-rep1.1x36mers.chrM.unique
zcat K562-RPS5_eCLIP_mock_input-human-ENCSR486QAE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS5_eCLIP_mock_input-human-ENCSR486QAE-rep1.1x36mers.chrM.unique
zcat K562-SAFB2-human-ENCSR943MHU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2-human-ENCSR943MHU-rep1.1x36mers.chrM.unique
zcat K562-SAFB2-human-ENCSR943MHU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2-human-ENCSR943MHU-rep2.1x36mers.chrM.unique
zcat K562-SAFB2_eCLIP_mock_input-human-ENCSR978JXM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2_eCLIP_mock_input-human-ENCSR978JXM-rep1.1x36mers.chrM.unique
zcat K562-SBDS-human-ENCSR059CWF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS-human-ENCSR059CWF-rep1.1x36mers.chrM.unique
zcat K562-SBDS-human-ENCSR059CWF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS-human-ENCSR059CWF-rep2.1x36mers.chrM.unique
zcat K562-SBDS_eCLIP_mock_input-human-ENCSR038TMA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS_eCLIP_mock_input-human-ENCSR038TMA-rep1.1x36mers.chrM.unique
zcat K562-SERBP1-human-ENCSR121GQH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1-human-ENCSR121GQH-rep1.1x36mers.chrM.unique
zcat K562-SERBP1-human-ENCSR121GQH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1-human-ENCSR121GQH-rep2.1x36mers.chrM.unique
zcat K562-SERBP1_eCLIP_mock_input-human-ENCSR752YLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1_eCLIP_mock_input-human-ENCSR752YLF-rep1.1x36mers.chrM.unique
zcat K562-SF3B1-human-ENCSR133QEA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1-human-ENCSR133QEA-rep1.1x36mers.chrM.unique
zcat K562-SF3B1-human-ENCSR133QEA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1-human-ENCSR133QEA-rep2.1x36mers.chrM.unique
zcat K562-SF3B1_eCLIP_mock_input-human-ENCSR496UBM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1_eCLIP_mock_input-human-ENCSR496UBM-rep1.1x36mers.chrM.unique
zcat K562-SF3B4-human-ENCSR267OLV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4-human-ENCSR267OLV-rep1.1x36mers.chrM.unique
zcat K562-SF3B4-human-ENCSR267OLV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4-human-ENCSR267OLV-rep2.1x36mers.chrM.unique
zcat K562-SF3B4_eCLIP_mock_input-human-ENCSR305KNE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4_eCLIP_mock_input-human-ENCSR305KNE-rep1.1x36mers.chrM.unique
zcat K562-SLBP-human-ENCSR483NOP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP-human-ENCSR483NOP-rep1.1x36mers.chrM.unique
zcat K562-SLBP-human-ENCSR483NOP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP-human-ENCSR483NOP-rep2.1x36mers.chrM.unique
zcat K562-SLBP_eCLIP_mock_input-human-ENCSR950WBG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP_eCLIP_mock_input-human-ENCSR950WBG-rep1.1x36mers.chrM.unique
zcat K562-SLTM-human-ENCSR000SSH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM-human-ENCSR000SSH-rep1.1x36mers.chrM.unique
zcat K562-SLTM-human-ENCSR000SSH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM-human-ENCSR000SSH-rep2.1x36mers.chrM.unique
zcat K562-SLTM_eCLIP_mock_input-human-ENCSR820GBM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM_eCLIP_mock_input-human-ENCSR820GBM-rep1.1x36mers.chrM.unique
zcat K562-SMNDC1-human-ENCSR658IQB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1-human-ENCSR658IQB-rep1.1x36mers.chrM.unique
zcat K562-SMNDC1-human-ENCSR658IQB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1-human-ENCSR658IQB-rep2.1x36mers.chrM.unique
zcat K562-SMNDC1_eCLIP_mock_input-human-ENCSR631CJA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1_eCLIP_mock_input-human-ENCSR631CJA-rep1.1x36mers.chrM.unique
zcat K562-SND1-human-ENCSR128VXC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1-human-ENCSR128VXC-rep1.1x36mers.chrM.unique
zcat K562-SND1-human-ENCSR128VXC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1-human-ENCSR128VXC-rep2.1x36mers.chrM.unique
zcat K562-SND1_eCLIP_mock_input-human-ENCSR435EVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1_eCLIP_mock_input-human-ENCSR435EVK-rep1.1x36mers.chrM.unique
zcat K562-SRSF1-human-ENCSR432XUP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1-human-ENCSR432XUP-rep1.1x36mers.chrM.unique
zcat K562-SRSF1-human-ENCSR432XUP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1-human-ENCSR432XUP-rep2.1x36mers.chrM.unique
zcat K562-SRSF1_eCLIP_mock_input-human-ENCSR925TYQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1_eCLIP_mock_input-human-ENCSR925TYQ-rep1.1x36mers.chrM.unique
zcat K562-SRSF7-human-ENCSR468FSW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7-human-ENCSR468FSW-rep1.1x36mers.chrM.unique
zcat K562-SRSF7-human-ENCSR468FSW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7-human-ENCSR468FSW-rep2.1x36mers.chrM.unique
zcat K562-SRSF7_eCLIP_mock_input-human-ENCSR145PHJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7_eCLIP_mock_input-human-ENCSR145PHJ-rep1.1x36mers.chrM.unique
zcat K562-TAF15-human-ENCSR568DZW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15-human-ENCSR568DZW-rep1.1x36mers.chrM.unique
zcat K562-TAF15-human-ENCSR568DZW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15-human-ENCSR568DZW-rep2.1x36mers.chrM.unique
zcat K562-TAF15_eCLIP_mock_input-human-ENCSR653CNZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15_eCLIP_mock_input-human-ENCSR653CNZ-rep1.1x36mers.chrM.unique
zcat K562-TARDBP-human-ENCSR584TCR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP-human-ENCSR584TCR-rep1.1x36mers.chrM.unique
zcat K562-TARDBP-human-ENCSR584TCR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP-human-ENCSR584TCR-rep2.1x36mers.chrM.unique
zcat K562-TARDBP_eCLIP_mock_input-human-ENCSR924OLO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP_eCLIP_mock_input-human-ENCSR924OLO-rep1.1x36mers.chrM.unique
zcat K562-TBRG4-human-ENCSR506OTC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4-human-ENCSR506OTC-rep1.1x36mers.chrM.unique
zcat K562-TBRG4-human-ENCSR506OTC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4-human-ENCSR506OTC-rep2.1x36mers.chrM.unique
zcat K562-TBRG4_eCLIP_mock_input-human-ENCSR512EZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4_eCLIP_mock_input-human-ENCSR512EZA-rep1.1x36mers.chrM.unique
zcat K562-TIA1-human-ENCSR057DWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1-human-ENCSR057DWB-rep1.1x36mers.chrM.unique
zcat K562-TIA1-human-ENCSR057DWB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1-human-ENCSR057DWB-rep2.1x36mers.chrM.unique
zcat K562-TIA1_eCLIP_mock_input-human-ENCSR356GCJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1_eCLIP_mock_input-human-ENCSR356GCJ-rep1.1x36mers.chrM.unique
zcat K562-TNRC6A_eCLIP_mock_input-human-ENCSR800LOQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TNRC6A_eCLIP_mock_input-human-ENCSR800LOQ-rep1.1x36mers.chrM.unique
zcat K562-TRA2A-human-ENCSR365NVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A-human-ENCSR365NVO-rep1.1x36mers.chrM.unique
zcat K562-TRA2A-human-ENCSR365NVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A-human-ENCSR365NVO-rep2.1x36mers.chrM.unique
zcat K562-TRA2A_eCLIP_mock_input-human-ENCSR619RLC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A_eCLIP_mock_input-human-ENCSR619RLC-rep1.1x36mers.chrM.unique
zcat K562-TROVE2-human-ENCSR539ZTS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2-human-ENCSR539ZTS-rep1.1x36mers.chrM.unique
zcat K562-TROVE2-human-ENCSR539ZTS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2-human-ENCSR539ZTS-rep2.1x36mers.chrM.unique
zcat K562-TROVE2_eCLIP_mock_input-human-ENCSR687GJH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2_eCLIP_mock_input-human-ENCSR687GJH-rep1.1x36mers.chrM.unique
zcat K562-U2AF1-human-ENCSR862QCH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1-human-ENCSR862QCH-rep1.1x36mers.chrM.unique
zcat K562-U2AF1-human-ENCSR862QCH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1-human-ENCSR862QCH-rep2.1x36mers.chrM.unique
zcat K562-U2AF1_eCLIP_mock_input-human-ENCSR482ZSE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1_eCLIP_mock_input-human-ENCSR482ZSE-rep1.1x36mers.chrM.unique
zcat K562-U2AF2-human-ENCSR893RAV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2-human-ENCSR893RAV-rep1.1x36mers.chrM.unique
zcat K562-U2AF2-human-ENCSR893RAV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2-human-ENCSR893RAV-rep2.1x36mers.chrM.unique
zcat K562-U2AF2_eCLIP_mock_input-human-ENCSR871RTL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2_eCLIP_mock_input-human-ENCSR871RTL-rep1.1x36mers.chrM.unique
zcat K562-UCHL5-human-ENCSR349KMG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5-human-ENCSR349KMG-rep1.1x36mers.chrM.unique
zcat K562-UCHL5-human-ENCSR349KMG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5-human-ENCSR349KMG-rep2.1x36mers.chrM.unique
zcat K562-UCHL5_eCLIP_mock_input-human-ENCSR751CSY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5_eCLIP_mock_input-human-ENCSR751CSY-rep1.1x36mers.chrM.unique
zcat K562-UPF1-human-ENCSR456ASB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1-human-ENCSR456ASB-rep1.1x36mers.chrM.unique
zcat K562-UPF1-human-ENCSR456ASB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1-human-ENCSR456ASB-rep2.1x36mers.chrM.unique
zcat K562-UPF1_eCLIP_mock_input-human-ENCSR461LGW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1_eCLIP_mock_input-human-ENCSR461LGW-rep1.1x36mers.chrM.unique
zcat K562-XRCC6-human-ENCSR258QKO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6-human-ENCSR258QKO-rep1.1x36mers.chrM.unique
zcat K562-XRCC6-human-ENCSR258QKO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6-human-ENCSR258QKO-rep2.1x36mers.chrM.unique
zcat K562-XRCC6_eCLIP_mock_input-human-ENCSR687HHB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6_eCLIP_mock_input-human-ENCSR687HHB-rep1.1x36mers.chrM.unique
zcat K562-XRN2-human-ENCSR657TZB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2-human-ENCSR657TZB-rep1.1x36mers.chrM.unique
zcat K562-XRN2-human-ENCSR657TZB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2-human-ENCSR657TZB-rep2.1x36mers.chrM.unique
zcat K562-XRN2_eCLIP_mock_input-human-ENCSR170XQH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2_eCLIP_mock_input-human-ENCSR170XQH-rep1.1x36mers.chrM.unique
zcat K562-YBX3-human-ENCSR529FKI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3-human-ENCSR529FKI-rep1.1x36mers.chrM.unique
zcat K562-YBX3-human-ENCSR529FKI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3-human-ENCSR529FKI-rep2.1x36mers.chrM.unique
zcat K562-YBX3_eCLIP_mock_input-human-ENCSR660VTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3_eCLIP_mock_input-human-ENCSR660VTT-rep1.1x36mers.chrM.unique
zcat K562-YWHAG-human-ENCSR867ZVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG-human-ENCSR867ZVK-rep1.1x36mers.chrM.unique
zcat K562-YWHAG-human-ENCSR867ZVK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG-human-ENCSR867ZVK-rep2.1x36mers.chrM.unique
zcat K562-YWHAG_eCLIP_mock_input-human-ENCSR812PBU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG_eCLIP_mock_input-human-ENCSR812PBU-rep1.1x36mers.chrM.unique
zcat K562-ZC3H11A-human-ENCSR712IAG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A-human-ENCSR712IAG-rep1.1x36mers.chrM.unique
zcat K562-ZC3H11A-human-ENCSR712IAG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A-human-ENCSR712IAG-rep2.1x36mers.chrM.unique
zcat K562-ZC3H11A_eCLIP_mock_input-human-ENCSR321GBR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A_eCLIP_mock_input-human-ENCSR321GBR-rep1.1x36mers.chrM.unique
zcat K562-ZNF622-human-ENCSR657TZZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622-human-ENCSR657TZZ-rep1.1x36mers.chrM.unique
zcat K562-ZNF622-human-ENCSR657TZZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622-human-ENCSR657TZZ-rep2.1x36mers.chrM.unique
zcat K562-ZNF622_eCLIP_mock_input-human-ENCSR594RFP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622_eCLIP_mock_input-human-ENCSR594RFP-rep1.1x36mers.chrM.unique
zcat K562-ZRANB2-human-ENCSR663NRA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2-human-ENCSR663NRA-rep1.1x36mers.chrM.unique
zcat K562-ZRANB2-human-ENCSR663NRA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2-human-ENCSR663NRA-rep2.1x36mers.chrM.unique
zcat K562-ZRANB2_eCLIP_mock_input-human-ENCSR528HOM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2_eCLIP_mock_input-human-ENCSR528HOM-rep1.1x36mers.chrM.unique
zcat adrenal_gland-DGCR8-human-ENCSR634MFO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8-human-ENCSR634MFO-rep1.1x36mers.chrM.unique
zcat adrenal_gland-DGCR8-human-ENCSR634MFO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8-human-ENCSR634MFO-rep2.1x36mers.chrM.unique
zcat adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep1.1x36mers.chrM.unique
zcat adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep2.1x36mers.chrM.unique
zcat adrenal_gland-HNRNPU-human-ENCSR368GER-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU-human-ENCSR368GER-rep1.1x36mers.chrM.unique
zcat adrenal_gland-HNRNPU-human-ENCSR368GER-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU-human-ENCSR368GER-rep2.1x36mers.chrM.unique
zcat adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep1.1x36mers.chrM.unique
zcat adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep2.1x36mers.chrM.unique
zcat HepG2-AGGF1-human-ENCSR543TPH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1-human-ENCSR543TPH-rep1.1x25mers.chrM.unique
zcat HepG2-AGGF1-human-ENCSR543TPH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1-human-ENCSR543TPH-rep2.1x25mers.chrM.unique
zcat HepG2-AGGF1_eCLIP_mock_input-human-ENCSR182AEG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-AGGF1_eCLIP_mock_input-human-ENCSR182AEG-rep1.1x25mers.chrM.unique
zcat HepG2-BCCIP-human-ENCSR485QCG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP-human-ENCSR485QCG-rep1.1x25mers.chrM.unique
zcat HepG2-BCCIP-human-ENCSR485QCG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP-human-ENCSR485QCG-rep2.1x25mers.chrM.unique
zcat HepG2-BCCIP_eCLIP_mock_input-human-ENCSR655BRZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BCCIP_eCLIP_mock_input-human-ENCSR655BRZ-rep1.1x25mers.chrM.unique
zcat HepG2-BUD13-human-ENCSR830BSQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13-human-ENCSR830BSQ-rep1.1x25mers.chrM.unique
zcat HepG2-BUD13-human-ENCSR830BSQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13-human-ENCSR830BSQ-rep2.1x25mers.chrM.unique
zcat HepG2-BUD13_eCLIP_mock_input-human-ENCSR777PDA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-BUD13_eCLIP_mock_input-human-ENCSR777PDA-rep1.1x25mers.chrM.unique
zcat HepG2-CDC40-human-ENCSR815VVI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40-human-ENCSR815VVI-rep1.1x25mers.chrM.unique
zcat HepG2-CDC40-human-ENCSR815VVI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40-human-ENCSR815VVI-rep2.1x25mers.chrM.unique
zcat HepG2-CDC40_eCLIP_mock_input-human-ENCSR828ALT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CDC40_eCLIP_mock_input-human-ENCSR828ALT-rep1.1x25mers.chrM.unique
zcat HepG2-CSTF2-human-ENCSR384MWO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2-human-ENCSR384MWO-rep1.1x25mers.chrM.unique
zcat HepG2-CSTF2-human-ENCSR384MWO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2-human-ENCSR384MWO-rep2.1x25mers.chrM.unique
zcat HepG2-CSTF2T-human-ENCSR919HSE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T-human-ENCSR919HSE-rep1.1x25mers.chrM.unique
zcat HepG2-CSTF2T-human-ENCSR919HSE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T-human-ENCSR919HSE-rep2.1x25mers.chrM.unique
zcat HepG2-CSTF2T_eCLIP_mock_input-human-ENCSR391GLS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2T_eCLIP_mock_input-human-ENCSR391GLS-rep1.1x25mers.chrM.unique
zcat HepG2-CSTF2_eCLIP_mock_input-human-ENCSR309GHK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-CSTF2_eCLIP_mock_input-human-ENCSR309GHK-rep1.1x25mers.chrM.unique
zcat HepG2-DDX20_eCLIP_mock_input-human-ENCSR240ZFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX20_eCLIP_mock_input-human-ENCSR240ZFU-rep1.1x25mers.chrM.unique
zcat HepG2-DDX3X-human-ENCSR648LAH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X-human-ENCSR648LAH-rep1.1x25mers.chrM.unique
zcat HepG2-DDX3X-human-ENCSR648LAH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X-human-ENCSR648LAH-rep2.1x25mers.chrM.unique
zcat HepG2-DDX3X_eCLIP_mock_input-human-ENCSR090VXV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX3X_eCLIP_mock_input-human-ENCSR090VXV-rep1.1x25mers.chrM.unique
zcat HepG2-DDX55-human-ENCSR845VGB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55-human-ENCSR845VGB-rep1.1x25mers.chrM.unique
zcat HepG2-DDX55-human-ENCSR845VGB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55-human-ENCSR845VGB-rep2.1x25mers.chrM.unique
zcat HepG2-DDX55_eCLIP_mock_input-human-ENCSR454OFD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX55_eCLIP_mock_input-human-ENCSR454OFD-rep1.1x25mers.chrM.unique
zcat HepG2-DDX59-human-ENCSR214BZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59-human-ENCSR214BZA-rep1.1x25mers.chrM.unique
zcat HepG2-DDX59-human-ENCSR214BZA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59-human-ENCSR214BZA-rep2.1x25mers.chrM.unique
zcat HepG2-DDX59_eCLIP_mock_input-human-ENCSR334OMC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX59_eCLIP_mock_input-human-ENCSR334OMC-rep1.1x25mers.chrM.unique
zcat HepG2-DDX6-human-ENCSR141OIM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6-human-ENCSR141OIM-rep1.1x25mers.chrM.unique
zcat HepG2-DDX6-human-ENCSR141OIM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6-human-ENCSR141OIM-rep2.1x25mers.chrM.unique
zcat HepG2-DDX6_eCLIP_mock_input-human-ENCSR099KAK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DDX6_eCLIP_mock_input-human-ENCSR099KAK-rep1.1x25mers.chrM.unique
zcat HepG2-DGCR8-human-ENCSR061SZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8-human-ENCSR061SZV-rep1.1x25mers.chrM.unique
zcat HepG2-DGCR8-human-ENCSR061SZV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8-human-ENCSR061SZV-rep2.1x25mers.chrM.unique
zcat HepG2-DGCR8_eCLIP_mock_input-human-ENCSR298SAD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DGCR8_eCLIP_mock_input-human-ENCSR298SAD-rep1.1x25mers.chrM.unique
zcat HepG2-DHX30-human-ENCSR565DGW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30-human-ENCSR565DGW-rep1.1x25mers.chrM.unique
zcat HepG2-DHX30-human-ENCSR565DGW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30-human-ENCSR565DGW-rep2.1x25mers.chrM.unique
zcat HepG2-DHX30_eCLIP_mock_input-human-ENCSR151MPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DHX30_eCLIP_mock_input-human-ENCSR151MPZ-rep1.1x25mers.chrM.unique
zcat HepG2-DKC1-human-ENCSR301TFY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1-human-ENCSR301TFY-rep1.1x25mers.chrM.unique
zcat HepG2-DKC1-human-ENCSR301TFY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1-human-ENCSR301TFY-rep2.1x25mers.chrM.unique
zcat HepG2-DKC1_eCLIP_mock_input-human-ENCSR197LHH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DKC1_eCLIP_mock_input-human-ENCSR197LHH-rep1.1x25mers.chrM.unique
zcat HepG2-DROSHA-human-ENCSR834YLD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA-human-ENCSR834YLD-rep1.1x25mers.chrM.unique
zcat HepG2-DROSHA-human-ENCSR834YLD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA-human-ENCSR834YLD-rep2.1x25mers.chrM.unique
zcat HepG2-DROSHA_eCLIP_mock_input-human-ENCSR785VKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-DROSHA_eCLIP_mock_input-human-ENCSR785VKF-rep1.1x25mers.chrM.unique
zcat HepG2-EFTUD2-human-ENCSR527DXF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2-human-ENCSR527DXF-rep1.1x25mers.chrM.unique
zcat HepG2-EFTUD2-human-ENCSR527DXF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2-human-ENCSR527DXF-rep2.1x25mers.chrM.unique
zcat HepG2-EFTUD2_eCLIP_mock_input-human-ENCSR878HWU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EFTUD2_eCLIP_mock_input-human-ENCSR878HWU-rep1.1x25mers.chrM.unique
zcat HepG2-EIF3D-human-ENCSR041NUV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D-human-ENCSR041NUV-rep1.1x25mers.chrM.unique
zcat HepG2-EIF3D-human-ENCSR041NUV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D-human-ENCSR041NUV-rep2.1x25mers.chrM.unique
zcat HepG2-EIF3D_eCLIP_mock_input-human-ENCSR755PSW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3D_eCLIP_mock_input-human-ENCSR755PSW-rep1.1x25mers.chrM.unique
zcat HepG2-EIF3H-human-ENCSR916XIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H-human-ENCSR916XIV-rep1.1x25mers.chrM.unique
zcat HepG2-EIF3H-human-ENCSR916XIV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H-human-ENCSR916XIV-rep2.1x25mers.chrM.unique
zcat HepG2-EIF3H_eCLIP_mock_input-human-ENCSR756NPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-EIF3H_eCLIP_mock_input-human-ENCSR756NPZ-rep1.1x25mers.chrM.unique
zcat HepG2-FAM120A-human-ENCSR987NYS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A-human-ENCSR987NYS-rep1.1x25mers.chrM.unique
zcat HepG2-FAM120A-human-ENCSR987NYS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A-human-ENCSR987NYS-rep2.1x25mers.chrM.unique
zcat HepG2-FAM120A_eCLIP_mock_input-human-ENCSR839KAX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FAM120A_eCLIP_mock_input-human-ENCSR839KAX-rep1.1x25mers.chrM.unique
zcat HepG2-FASTKD2-human-ENCSR023UHL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2-human-ENCSR023UHL-rep1.1x25mers.chrM.unique
zcat HepG2-FASTKD2-human-ENCSR023UHL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2-human-ENCSR023UHL-rep2.1x25mers.chrM.unique
zcat HepG2-FASTKD2_eCLIP_mock_input-human-ENCSR671FKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FASTKD2_eCLIP_mock_input-human-ENCSR671FKF-rep1.1x25mers.chrM.unique
zcat HepG2-FKBP4-human-ENCSR018ZUE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4-human-ENCSR018ZUE-rep1.1x25mers.chrM.unique
zcat HepG2-FKBP4-human-ENCSR018ZUE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4-human-ENCSR018ZUE-rep2.1x25mers.chrM.unique
zcat HepG2-FKBP4_eCLIP_mock_input-human-ENCSR704LTK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FKBP4_eCLIP_mock_input-human-ENCSR704LTK-rep1.1x25mers.chrM.unique
zcat HepG2-FUBP3-human-ENCSR486YGP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3-human-ENCSR486YGP-rep1.1x25mers.chrM.unique
zcat HepG2-FUBP3-human-ENCSR486YGP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3-human-ENCSR486YGP-rep2.1x25mers.chrM.unique
zcat HepG2-FUBP3_eCLIP_mock_input-human-ENCSR056RZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-FUBP3_eCLIP_mock_input-human-ENCSR056RZV-rep1.1x25mers.chrM.unique
zcat HepG2-GRSF1-human-ENCSR668MJX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1-human-ENCSR668MJX-rep1.1x25mers.chrM.unique
zcat HepG2-GRSF1-human-ENCSR668MJX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1-human-ENCSR668MJX-rep2.1x25mers.chrM.unique
zcat HepG2-GRSF1_eCLIP_mock_input-human-ENCSR638YHN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRSF1_eCLIP_mock_input-human-ENCSR638YHN-rep1.1x25mers.chrM.unique
zcat HepG2-GRWD1-human-ENCSR893NWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1-human-ENCSR893NWB-rep1.1x25mers.chrM.unique
zcat HepG2-GRWD1-human-ENCSR893NWB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1-human-ENCSR893NWB-rep2.1x25mers.chrM.unique
zcat HepG2-GRWD1_eCLIP_mock_input-human-ENCSR835ZOK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GRWD1_eCLIP_mock_input-human-ENCSR835ZOK-rep1.1x25mers.chrM.unique
zcat HepG2-GTF2F1-human-ENCSR265ZIS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1-human-ENCSR265ZIS-rep1.1x25mers.chrM.unique
zcat HepG2-GTF2F1-human-ENCSR265ZIS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1-human-ENCSR265ZIS-rep2.1x25mers.chrM.unique
zcat HepG2-GTF2F1_eCLIP_mock_input-human-ENCSR451HMR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-GTF2F1_eCLIP_mock_input-human-ENCSR451HMR-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPA1-human-ENCSR769UEW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1-human-ENCSR769UEW-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPA1-human-ENCSR769UEW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1-human-ENCSR769UEW-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPA1_eCLIP_mock_input-human-ENCSR110XNS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPA1_eCLIP_mock_input-human-ENCSR110XNS-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPC-human-ENCSR550DVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC-human-ENCSR550DVK-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPC-human-ENCSR550DVK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC-human-ENCSR550DVK-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPC_eCLIP_mock_input-human-ENCSR497ANA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPC_eCLIP_mock_input-human-ENCSR497ANA-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPK-human-ENCSR828ZID-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK-human-ENCSR828ZID-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPK-human-ENCSR828ZID-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK-human-ENCSR828ZID-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPK_eCLIP_mock_input-human-ENCSR354KAS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPK_eCLIP_mock_input-human-ENCSR354KAS-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPL-human-ENCSR724RDN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL-human-ENCSR724RDN-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPL-human-ENCSR724RDN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL-human-ENCSR724RDN-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPL_eCLIP_mock_input-human-ENCSR513UTE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPL_eCLIP_mock_input-human-ENCSR513UTE-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPM-human-ENCSR267UCX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM-human-ENCSR267UCX-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPM-human-ENCSR267UCX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM-human-ENCSR267UCX-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPM_eCLIP_mock_input-human-ENCSR459ONR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPM_eCLIP_mock_input-human-ENCSR459ONR-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPU-human-ENCSR240MVJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU-human-ENCSR240MVJ-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPU-human-ENCSR240MVJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU-human-ENCSR240MVJ-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPUL1-human-ENCSR755TJC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1-human-ENCSR755TJC-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPUL1-human-ENCSR755TJC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1-human-ENCSR755TJC-rep2.1x25mers.chrM.unique
zcat HepG2-HNRNPUL1_eCLIP_mock_input-human-ENCSR643JMB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPUL1_eCLIP_mock_input-human-ENCSR643JMB-rep1.1x25mers.chrM.unique
zcat HepG2-HNRNPU_eCLIP_mock_input-human-ENCSR614VYQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-HNRNPU_eCLIP_mock_input-human-ENCSR614VYQ-rep1.1x25mers.chrM.unique
zcat HepG2-IGF2BP1-human-ENCSR744GEU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1-human-ENCSR744GEU-rep1.1x25mers.chrM.unique
zcat HepG2-IGF2BP1-human-ENCSR744GEU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1-human-ENCSR744GEU-rep2.1x25mers.chrM.unique
zcat HepG2-IGF2BP1_eCLIP_mock_input-human-ENCSR205ZCE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP1_eCLIP_mock_input-human-ENCSR205ZCE-rep1.1x25mers.chrM.unique
zcat HepG2-IGF2BP3-human-ENCSR993OLA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3-human-ENCSR993OLA-rep1.1x25mers.chrM.unique
zcat HepG2-IGF2BP3-human-ENCSR993OLA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3-human-ENCSR993OLA-rep2.1x25mers.chrM.unique
zcat HepG2-IGF2BP3_eCLIP_mock_input-human-ENCSR077KVG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-IGF2BP3_eCLIP_mock_input-human-ENCSR077KVG-rep1.1x25mers.chrM.unique
zcat HepG2-ILF3-human-ENCSR786TSC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3-human-ENCSR786TSC-rep1.1x25mers.chrM.unique
zcat HepG2-ILF3-human-ENCSR786TSC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3-human-ENCSR786TSC-rep2.1x25mers.chrM.unique
zcat HepG2-ILF3_eCLIP_mock_input-human-ENCSR080OLK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ILF3_eCLIP_mock_input-human-ENCSR080OLK-rep1.1x25mers.chrM.unique
zcat HepG2-LARP4-human-ENCSR805SRN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4-human-ENCSR805SRN-rep1.1x25mers.chrM.unique
zcat HepG2-LARP4-human-ENCSR805SRN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4-human-ENCSR805SRN-rep2.1x25mers.chrM.unique
zcat HepG2-LARP4_eCLIP_mock_input-human-ENCSR192PUP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP4_eCLIP_mock_input-human-ENCSR192PUP-rep1.1x25mers.chrM.unique
zcat HepG2-LARP7-human-ENCSR961OKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7-human-ENCSR961OKA-rep1.1x25mers.chrM.unique
zcat HepG2-LARP7-human-ENCSR961OKA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7-human-ENCSR961OKA-rep2.1x25mers.chrM.unique
zcat HepG2-LARP7_eCLIP_mock_input-human-ENCSR095SIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LARP7_eCLIP_mock_input-human-ENCSR095SIV-rep1.1x25mers.chrM.unique
zcat HepG2-LIN28B-human-ENCSR861GYE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B-human-ENCSR861GYE-rep1.1x25mers.chrM.unique
zcat HepG2-LIN28B-human-ENCSR861GYE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B-human-ENCSR861GYE-rep2.1x25mers.chrM.unique
zcat HepG2-LIN28B_eCLIP_mock_input-human-ENCSR746ZSV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LIN28B_eCLIP_mock_input-human-ENCSR746ZSV-rep1.1x25mers.chrM.unique
zcat HepG2-LSM11-human-ENCSR135VMS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11-human-ENCSR135VMS-rep1.1x25mers.chrM.unique
zcat HepG2-LSM11-human-ENCSR135VMS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11-human-ENCSR135VMS-rep2.1x25mers.chrM.unique
zcat HepG2-LSM11_eCLIP_mock_input-human-ENCSR114XBO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-LSM11_eCLIP_mock_input-human-ENCSR114XBO-rep1.1x25mers.chrM.unique
zcat HepG2-MATR3-human-ENCSR290VLT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3-human-ENCSR290VLT-rep1.1x25mers.chrM.unique
zcat HepG2-MATR3-human-ENCSR290VLT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3-human-ENCSR290VLT-rep2.1x25mers.chrM.unique
zcat HepG2-MATR3_eCLIP_mock_input-human-ENCSR438XYI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-MATR3_eCLIP_mock_input-human-ENCSR438XYI-rep1.1x25mers.chrM.unique
zcat HepG2-NCBP2-human-ENCSR018RVZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2-human-ENCSR018RVZ-rep1.1x25mers.chrM.unique
zcat HepG2-NCBP2-human-ENCSR018RVZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2-human-ENCSR018RVZ-rep2.1x25mers.chrM.unique
zcat HepG2-NCBP2_eCLIP_mock_input-human-ENCSR257OYO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NCBP2_eCLIP_mock_input-human-ENCSR257OYO-rep1.1x25mers.chrM.unique
zcat HepG2-NKRF-human-ENCSR277DEO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF-human-ENCSR277DEO-rep1.1x25mers.chrM.unique
zcat HepG2-NKRF-human-ENCSR277DEO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF-human-ENCSR277DEO-rep2.1x25mers.chrM.unique
zcat HepG2-NKRF_eCLIP_mock_input-human-ENCSR479XOI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NKRF_eCLIP_mock_input-human-ENCSR479XOI-rep1.1x25mers.chrM.unique
zcat HepG2-NOL12-human-ENCSR820DQJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12-human-ENCSR820DQJ-rep1.1x25mers.chrM.unique
zcat HepG2-NOL12-human-ENCSR820DQJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12-human-ENCSR820DQJ-rep2.1x25mers.chrM.unique
zcat HepG2-NOL12_eCLIP_mock_input-human-ENCSR709ABG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOL12_eCLIP_mock_input-human-ENCSR709ABG-rep1.1x25mers.chrM.unique
zcat HepG2-NOLC1-human-ENCSR194HZU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1-human-ENCSR194HZU-rep1.1x25mers.chrM.unique
zcat HepG2-NOLC1-human-ENCSR194HZU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1-human-ENCSR194HZU-rep2.1x25mers.chrM.unique
zcat HepG2-NOLC1_eCLIP_mock_input-human-ENCSR278BZH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-NOLC1_eCLIP_mock_input-human-ENCSR278BZH-rep1.1x25mers.chrM.unique
zcat HepG2-PCBP2-human-ENCSR339FUY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2-human-ENCSR339FUY-rep1.1x25mers.chrM.unique
zcat HepG2-PCBP2-human-ENCSR339FUY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2-human-ENCSR339FUY-rep2.1x25mers.chrM.unique
zcat HepG2-PCBP2_eCLIP_mock_input-human-ENCSR115GAA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PCBP2_eCLIP_mock_input-human-ENCSR115GAA-rep1.1x25mers.chrM.unique
zcat HepG2-POLR2G-human-ENCSR820WHR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G-human-ENCSR820WHR-rep1.1x25mers.chrM.unique
zcat HepG2-POLR2G-human-ENCSR820WHR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G-human-ENCSR820WHR-rep2.1x25mers.chrM.unique
zcat HepG2-POLR2G_eCLIP_mock_input-human-ENCSR129SCO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-POLR2G_eCLIP_mock_input-human-ENCSR129SCO-rep1.1x25mers.chrM.unique
zcat HepG2-PPIG-human-ENCSR097NEE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG-human-ENCSR097NEE-rep1.1x25mers.chrM.unique
zcat HepG2-PPIG-human-ENCSR097NEE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG-human-ENCSR097NEE-rep2.1x25mers.chrM.unique
zcat HepG2-PPIG_eCLIP_mock_input-human-ENCSR445LJH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PPIG_eCLIP_mock_input-human-ENCSR445LJH-rep1.1x25mers.chrM.unique
zcat HepG2-PRPF8-human-ENCSR121NVA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8-human-ENCSR121NVA-rep1.1x25mers.chrM.unique
zcat HepG2-PRPF8-human-ENCSR121NVA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8-human-ENCSR121NVA-rep2.1x25mers.chrM.unique
zcat HepG2-PRPF8_eCLIP_mock_input-human-ENCSR565KBR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PRPF8_eCLIP_mock_input-human-ENCSR565KBR-rep1.1x25mers.chrM.unique
zcat HepG2-PTBP1-human-ENCSR384KAN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1-human-ENCSR384KAN-rep1.1x25mers.chrM.unique
zcat HepG2-PTBP1-human-ENCSR384KAN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1-human-ENCSR384KAN-rep2.1x25mers.chrM.unique
zcat HepG2-PTBP1_eCLIP_mock_input-human-ENCSR438NCK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-PTBP1_eCLIP_mock_input-human-ENCSR438NCK-rep1.1x25mers.chrM.unique
zcat HepG2-QKI-human-ENCSR570WLM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI-human-ENCSR570WLM-rep1.1x25mers.chrM.unique
zcat HepG2-QKI-human-ENCSR570WLM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI-human-ENCSR570WLM-rep2.1x25mers.chrM.unique
zcat HepG2-QKI_eCLIP_mock_input-human-ENCSR130TOJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-QKI_eCLIP_mock_input-human-ENCSR130TOJ-rep1.1x25mers.chrM.unique
zcat HepG2-RBFOX2-human-ENCSR987FTF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2-human-ENCSR987FTF-rep1.1x25mers.chrM.unique
zcat HepG2-RBFOX2-human-ENCSR987FTF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2-human-ENCSR987FTF-rep2.1x25mers.chrM.unique
zcat HepG2-RBFOX2_eCLIP_mock_input-human-ENCSR799EKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBFOX2_eCLIP_mock_input-human-ENCSR799EKA-rep1.1x25mers.chrM.unique
zcat HepG2-RBM15-human-ENCSR754NDA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15-human-ENCSR754NDA-rep1.1x25mers.chrM.unique
zcat HepG2-RBM15-human-ENCSR754NDA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15-human-ENCSR754NDA-rep2.1x25mers.chrM.unique
zcat HepG2-RBM15_eCLIP_mock_input-human-ENCSR317PWQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM15_eCLIP_mock_input-human-ENCSR317PWQ-rep1.1x25mers.chrM.unique
zcat HepG2-RBM22-human-ENCSR456JJQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22-human-ENCSR456JJQ-rep1.1x25mers.chrM.unique
zcat HepG2-RBM22-human-ENCSR456JJQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22-human-ENCSR456JJQ-rep2.1x25mers.chrM.unique
zcat HepG2-RBM22_eCLIP_mock_input-human-ENCSR775UPS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM22_eCLIP_mock_input-human-ENCSR775UPS-rep1.1x25mers.chrM.unique
zcat HepG2-RBM5-human-ENCSR489ABS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5-human-ENCSR489ABS-rep1.1x25mers.chrM.unique
zcat HepG2-RBM5-human-ENCSR489ABS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5-human-ENCSR489ABS-rep2.1x25mers.chrM.unique
zcat HepG2-RBM5_eCLIP_mock_input-human-ENCSR414RME-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RBM5_eCLIP_mock_input-human-ENCSR414RME-rep1.1x25mers.chrM.unique
zcat HepG2-RPL23A_eCLIP_mock_input-human-ENCSR224ECB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPL23A_eCLIP_mock_input-human-ENCSR224ECB-rep1.1x25mers.chrM.unique
zcat HepG2-RPS3-human-ENCSR766FAC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3-human-ENCSR766FAC-rep1.1x25mers.chrM.unique
zcat HepG2-RPS3-human-ENCSR766FAC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3-human-ENCSR766FAC-rep2.1x25mers.chrM.unique
zcat HepG2-RPS3_eCLIP_mock_input-human-ENCSR745BIL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS3_eCLIP_mock_input-human-ENCSR745BIL-rep1.1x25mers.chrM.unique
zcat HepG2-RPS5_eCLIP_mock_input-human-ENCSR828MEJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-RPS5_eCLIP_mock_input-human-ENCSR828MEJ-rep1.1x25mers.chrM.unique
zcat HepG2-SF3A3-human-ENCSR331MIC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3-human-ENCSR331MIC-rep1.1x25mers.chrM.unique
zcat HepG2-SF3A3-human-ENCSR331MIC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3-human-ENCSR331MIC-rep2.1x25mers.chrM.unique
zcat HepG2-SF3A3_eCLIP_mock_input-human-ENCSR859PUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3A3_eCLIP_mock_input-human-ENCSR859PUB-rep1.1x25mers.chrM.unique
zcat HepG2-SF3B4-human-ENCSR279UJF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4-human-ENCSR279UJF-rep1.1x25mers.chrM.unique
zcat HepG2-SF3B4-human-ENCSR279UJF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4-human-ENCSR279UJF-rep2.1x25mers.chrM.unique
zcat HepG2-SF3B4_eCLIP_mock_input-human-ENCSR886YYD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SF3B4_eCLIP_mock_input-human-ENCSR886YYD-rep1.1x25mers.chrM.unique
zcat HepG2-SFPQ-human-ENCSR965DLL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ-human-ENCSR965DLL-rep1.1x25mers.chrM.unique
zcat HepG2-SFPQ-human-ENCSR965DLL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ-human-ENCSR965DLL-rep2.1x25mers.chrM.unique
zcat HepG2-SFPQ_eCLIP_mock_input-human-ENCSR506EIW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SFPQ_eCLIP_mock_input-human-ENCSR506EIW-rep1.1x25mers.chrM.unique
zcat HepG2-SLTM-human-ENCSR351PVI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM-human-ENCSR351PVI-rep1.1x25mers.chrM.unique
zcat HepG2-SLTM-human-ENCSR351PVI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM-human-ENCSR351PVI-rep2.1x25mers.chrM.unique
zcat HepG2-SLTM_eCLIP_mock_input-human-ENCSR670UPZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SLTM_eCLIP_mock_input-human-ENCSR670UPZ-rep1.1x25mers.chrM.unique
zcat HepG2-SMNDC1-human-ENCSR373ODC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1-human-ENCSR373ODC-rep1.1x25mers.chrM.unique
zcat HepG2-SMNDC1-human-ENCSR373ODC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1-human-ENCSR373ODC-rep2.1x25mers.chrM.unique
zcat HepG2-SMNDC1_eCLIP_mock_input-human-ENCSR388VKV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SMNDC1_eCLIP_mock_input-human-ENCSR388VKV-rep1.1x25mers.chrM.unique
zcat HepG2-SND1-human-ENCSR061EVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1-human-ENCSR061EVO-rep1.1x25mers.chrM.unique
zcat HepG2-SND1-human-ENCSR061EVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1-human-ENCSR061EVO-rep2.1x25mers.chrM.unique
zcat HepG2-SND1_eCLIP_mock_input-human-ENCSR167OYL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SND1_eCLIP_mock_input-human-ENCSR167OYL-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF1-human-ENCSR989VIY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1-human-ENCSR989VIY-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF1-human-ENCSR989VIY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1-human-ENCSR989VIY-rep2.1x25mers.chrM.unique
zcat HepG2-SRSF1_eCLIP_mock_input-human-ENCSR499ZCU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF1_eCLIP_mock_input-human-ENCSR499ZCU-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF7-human-ENCSR513NDD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7-human-ENCSR513NDD-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF7-human-ENCSR513NDD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7-human-ENCSR513NDD-rep2.1x25mers.chrM.unique
zcat HepG2-SRSF7_eCLIP_mock_input-human-ENCSR629MQN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF7_eCLIP_mock_input-human-ENCSR629MQN-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF9-human-ENCSR773KRC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9-human-ENCSR773KRC-rep1.1x25mers.chrM.unique
zcat HepG2-SRSF9-human-ENCSR773KRC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9-human-ENCSR773KRC-rep2.1x25mers.chrM.unique
zcat HepG2-SRSF9_eCLIP_mock_input-human-ENCSR060VZF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SRSF9_eCLIP_mock_input-human-ENCSR060VZF-rep1.1x25mers.chrM.unique
zcat HepG2-SUB1-human-ENCSR406OOZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1-human-ENCSR406OOZ-rep1.1x25mers.chrM.unique
zcat HepG2-SUB1-human-ENCSR406OOZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1-human-ENCSR406OOZ-rep2.1x25mers.chrM.unique
zcat HepG2-SUB1_eCLIP_mock_input-human-ENCSR641PRC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUB1_eCLIP_mock_input-human-ENCSR641PRC-rep1.1x25mers.chrM.unique
zcat HepG2-SUGP2-human-ENCSR506UPY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2-human-ENCSR506UPY-rep1.1x25mers.chrM.unique
zcat HepG2-SUGP2-human-ENCSR506UPY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2-human-ENCSR506UPY-rep2.1x25mers.chrM.unique
zcat HepG2-SUGP2_eCLIP_mock_input-human-ENCSR895TTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUGP2_eCLIP_mock_input-human-ENCSR895TTM-rep1.1x25mers.chrM.unique
zcat HepG2-SUPV3L1-human-ENCSR580MFX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1-human-ENCSR580MFX-rep1.1x25mers.chrM.unique
zcat HepG2-SUPV3L1-human-ENCSR580MFX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1-human-ENCSR580MFX-rep2.1x25mers.chrM.unique
zcat HepG2-SUPV3L1_eCLIP_mock_input-human-ENCSR376KLZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-SUPV3L1_eCLIP_mock_input-human-ENCSR376KLZ-rep1.1x25mers.chrM.unique
zcat HepG2-TAF15-human-ENCSR841EQA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15-human-ENCSR841EQA-rep1.1x25mers.chrM.unique
zcat HepG2-TAF15-human-ENCSR841EQA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15-human-ENCSR841EQA-rep2.1x25mers.chrM.unique
zcat HepG2-TAF15_eCLIP_mock_input-human-ENCSR708TCY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TAF15_eCLIP_mock_input-human-ENCSR708TCY-rep1.1x25mers.chrM.unique
zcat HepG2-TBRG4-human-ENCSR916SRV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4-human-ENCSR916SRV-rep1.1x25mers.chrM.unique
zcat HepG2-TBRG4-human-ENCSR916SRV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4-human-ENCSR916SRV-rep2.1x25mers.chrM.unique
zcat HepG2-TBRG4_eCLIP_mock_input-human-ENCSR081WUU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TBRG4_eCLIP_mock_input-human-ENCSR081WUU-rep1.1x25mers.chrM.unique
zcat HepG2-TIA1-human-ENCSR623VEQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1-human-ENCSR623VEQ-rep1.1x25mers.chrM.unique
zcat HepG2-TIA1-human-ENCSR623VEQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1-human-ENCSR623VEQ-rep2.1x25mers.chrM.unique
zcat HepG2-TIA1_eCLIP_mock_input-human-ENCSR333PZV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TIA1_eCLIP_mock_input-human-ENCSR333PZV-rep1.1x25mers.chrM.unique
zcat HepG2-TNRC6A_eCLIP_mock_input-human-ENCSR188OHK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TNRC6A_eCLIP_mock_input-human-ENCSR188OHK-rep1.1x25mers.chrM.unique
zcat HepG2-TRA2A-human-ENCSR314UMJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A-human-ENCSR314UMJ-rep1.1x25mers.chrM.unique
zcat HepG2-TRA2A-human-ENCSR314UMJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A-human-ENCSR314UMJ-rep2.1x25mers.chrM.unique
zcat HepG2-TRA2A_eCLIP_mock_input-human-ENCSR544CTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TRA2A_eCLIP_mock_input-human-ENCSR544CTM-rep1.1x25mers.chrM.unique
zcat HepG2-TROVE2-human-ENCSR993FMY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2-human-ENCSR993FMY-rep1.1x25mers.chrM.unique
zcat HepG2-TROVE2-human-ENCSR993FMY-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2-human-ENCSR993FMY-rep2.1x25mers.chrM.unique
zcat HepG2-TROVE2_eCLIP_mock_input-human-ENCSR619LRH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-TROVE2_eCLIP_mock_input-human-ENCSR619LRH-rep1.1x25mers.chrM.unique
zcat HepG2-U2AF1-human-ENCSR328LLU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1-human-ENCSR328LLU-rep1.1x25mers.chrM.unique
zcat HepG2-U2AF1-human-ENCSR328LLU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1-human-ENCSR328LLU-rep2.1x25mers.chrM.unique
zcat HepG2-U2AF1_eCLIP_mock_input-human-ENCSR941GJG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF1_eCLIP_mock_input-human-ENCSR941GJG-rep1.1x25mers.chrM.unique
zcat HepG2-U2AF2-human-ENCSR202BFN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2-human-ENCSR202BFN-rep1.1x25mers.chrM.unique
zcat HepG2-U2AF2-human-ENCSR202BFN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2-human-ENCSR202BFN-rep2.1x25mers.chrM.unique
zcat HepG2-U2AF2_eCLIP_mock_input-human-ENCSR049GND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-U2AF2_eCLIP_mock_input-human-ENCSR049GND-rep1.1x25mers.chrM.unique
zcat HepG2-UCHL5-human-ENCSR490IEE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5-human-ENCSR490IEE-rep1.1x25mers.chrM.unique
zcat HepG2-UCHL5-human-ENCSR490IEE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5-human-ENCSR490IEE-rep2.1x25mers.chrM.unique
zcat HepG2-UCHL5_eCLIP_mock_input-human-ENCSR161TFX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-UCHL5_eCLIP_mock_input-human-ENCSR161TFX-rep1.1x25mers.chrM.unique
zcat HepG2-XPO5-human-ENCSR921SXC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5-human-ENCSR921SXC-rep1.1x25mers.chrM.unique
zcat HepG2-XPO5-human-ENCSR921SXC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5-human-ENCSR921SXC-rep2.1x25mers.chrM.unique
zcat HepG2-XPO5_eCLIP_mock_input-human-ENCSR583KVR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XPO5_eCLIP_mock_input-human-ENCSR583KVR-rep1.1x25mers.chrM.unique
zcat HepG2-XRCC6-human-ENCSR571ROL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6-human-ENCSR571ROL-rep1.1x25mers.chrM.unique
zcat HepG2-XRCC6-human-ENCSR571ROL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6-human-ENCSR571ROL-rep2.1x25mers.chrM.unique
zcat HepG2-XRCC6_eCLIP_mock_input-human-ENCSR044NGV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRCC6_eCLIP_mock_input-human-ENCSR044NGV-rep1.1x25mers.chrM.unique
zcat HepG2-XRN2-human-ENCSR655NZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2-human-ENCSR655NZA-rep1.1x25mers.chrM.unique
zcat HepG2-XRN2-human-ENCSR655NZA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2-human-ENCSR655NZA-rep2.1x25mers.chrM.unique
zcat HepG2-XRN2_eCLIP_mock_input-human-ENCSR247PDK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-XRN2_eCLIP_mock_input-human-ENCSR247PDK-rep1.1x25mers.chrM.unique
zcat HepG2-ZC3H11A-human-ENCSR907GUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A-human-ENCSR907GUB-rep1.1x25mers.chrM.unique
zcat HepG2-ZC3H11A-human-ENCSR907GUB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A-human-ENCSR907GUB-rep2.1x25mers.chrM.unique
zcat HepG2-ZC3H11A_eCLIP_mock_input-human-ENCSR098VKQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - HepG2-ZC3H11A_eCLIP_mock_input-human-ENCSR098VKQ-rep1.1x25mers.chrM.unique
zcat K562-AARS-human-ENCSR825SVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS-human-ENCSR825SVO-rep1.1x25mers.chrM.unique
zcat K562-AARS-human-ENCSR825SVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS-human-ENCSR825SVO-rep2.1x25mers.chrM.unique
zcat K562-AARS_eCLIP_mock_input-human-ENCSR696PRX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AARS_eCLIP_mock_input-human-ENCSR696PRX-rep1.1x25mers.chrM.unique
zcat K562-AGGF1-human-ENCSR725ARB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1-human-ENCSR725ARB-rep1.1x25mers.chrM.unique
zcat K562-AGGF1-human-ENCSR725ARB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1-human-ENCSR725ARB-rep2.1x25mers.chrM.unique
zcat K562-AGGF1_eCLIP_mock_input-human-ENCSR910LAN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AGGF1_eCLIP_mock_input-human-ENCSR910LAN-rep1.1x25mers.chrM.unique
zcat K562-AKAP8L-human-ENCSR206RXT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L-human-ENCSR206RXT-rep1.1x25mers.chrM.unique
zcat K562-AKAP8L-human-ENCSR206RXT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L-human-ENCSR206RXT-rep2.1x25mers.chrM.unique
zcat K562-AKAP8L_eCLIP_mock_input-human-ENCSR550SGC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-AKAP8L_eCLIP_mock_input-human-ENCSR550SGC-rep1.1x25mers.chrM.unique
zcat K562-BUD13-human-ENCSR663WES-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13-human-ENCSR663WES-rep1.1x25mers.chrM.unique
zcat K562-BUD13-human-ENCSR663WES-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13-human-ENCSR663WES-rep2.1x25mers.chrM.unique
zcat K562-BUD13_eCLIP_mock_input-human-ENCSR736LKF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-BUD13_eCLIP_mock_input-human-ENCSR736LKF-rep1.1x25mers.chrM.unique
zcat K562-CPSF6-human-ENCSR532VUB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6-human-ENCSR532VUB-rep1.1x25mers.chrM.unique
zcat K562-CPSF6-human-ENCSR532VUB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6-human-ENCSR532VUB-rep2.1x25mers.chrM.unique
zcat K562-CPSF6_eCLIP_mock_input-human-ENCSR249WNK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CPSF6_eCLIP_mock_input-human-ENCSR249WNK-rep1.1x25mers.chrM.unique
zcat K562-CSTF2T-human-ENCSR840DRD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T-human-ENCSR840DRD-rep1.1x25mers.chrM.unique
zcat K562-CSTF2T-human-ENCSR840DRD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T-human-ENCSR840DRD-rep2.1x25mers.chrM.unique
zcat K562-CSTF2T_eCLIP_mock_input-human-ENCSR722LZB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-CSTF2T_eCLIP_mock_input-human-ENCSR722LZB-rep1.1x25mers.chrM.unique
zcat K562-DDX24-human-ENCSR999WKT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24-human-ENCSR999WKT-rep1.1x25mers.chrM.unique
zcat K562-DDX24-human-ENCSR999WKT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24-human-ENCSR999WKT-rep2.1x25mers.chrM.unique
zcat K562-DDX24_eCLIP_mock_input-human-ENCSR195IWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX24_eCLIP_mock_input-human-ENCSR195IWB-rep1.1x25mers.chrM.unique
zcat K562-DDX3X-human-ENCSR930BZL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X-human-ENCSR930BZL-rep1.1x25mers.chrM.unique
zcat K562-DDX3X-human-ENCSR930BZL-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X-human-ENCSR930BZL-rep2.1x25mers.chrM.unique
zcat K562-DDX3X_eCLIP_mock_input-human-ENCSR028CRL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX3X_eCLIP_mock_input-human-ENCSR028CRL-rep1.1x25mers.chrM.unique
zcat K562-DDX42-human-ENCSR576SHT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42-human-ENCSR576SHT-rep1.1x25mers.chrM.unique
zcat K562-DDX42-human-ENCSR576SHT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42-human-ENCSR576SHT-rep2.1x25mers.chrM.unique
zcat K562-DDX42_eCLIP_mock_input-human-ENCSR200SAU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX42_eCLIP_mock_input-human-ENCSR200SAU-rep1.1x25mers.chrM.unique
zcat K562-DDX55-human-ENCSR923NKN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55-human-ENCSR923NKN-rep1.1x25mers.chrM.unique
zcat K562-DDX55-human-ENCSR923NKN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55-human-ENCSR923NKN-rep2.1x25mers.chrM.unique
zcat K562-DDX55_eCLIP_mock_input-human-ENCSR180EJY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX55_eCLIP_mock_input-human-ENCSR180EJY-rep1.1x25mers.chrM.unique
zcat K562-DDX6-human-ENCSR893EFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6-human-ENCSR893EFU-rep1.1x25mers.chrM.unique
zcat K562-DDX6-human-ENCSR893EFU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6-human-ENCSR893EFU-rep2.1x25mers.chrM.unique
zcat K562-DDX6_eCLIP_mock_input-human-ENCSR207DWI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DDX6_eCLIP_mock_input-human-ENCSR207DWI-rep1.1x25mers.chrM.unique
zcat K562-DGCR8-human-ENCSR947JVR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8-human-ENCSR947JVR-rep1.1x25mers.chrM.unique
zcat K562-DGCR8-human-ENCSR947JVR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8-human-ENCSR947JVR-rep2.1x25mers.chrM.unique
zcat K562-DGCR8_eCLIP_mock_input-human-ENCSR616BTD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DGCR8_eCLIP_mock_input-human-ENCSR616BTD-rep1.1x25mers.chrM.unique
zcat K562-DHX30-human-ENCSR529GSJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30-human-ENCSR529GSJ-rep1.1x25mers.chrM.unique
zcat K562-DHX30-human-ENCSR529GSJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30-human-ENCSR529GSJ-rep2.1x25mers.chrM.unique
zcat K562-DHX30_eCLIP_mock_input-human-ENCSR224SND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DHX30_eCLIP_mock_input-human-ENCSR224SND-rep1.1x25mers.chrM.unique
zcat K562-DROSHA-human-ENCSR653HQC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA-human-ENCSR653HQC-rep1.1x25mers.chrM.unique
zcat K562-DROSHA-human-ENCSR653HQC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA-human-ENCSR653HQC-rep2.1x25mers.chrM.unique
zcat K562-DROSHA_eCLIP_mock_input-human-ENCSR828NSY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-DROSHA_eCLIP_mock_input-human-ENCSR828NSY-rep1.1x25mers.chrM.unique
zcat K562-EFTUD2-human-ENCSR844RVX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2-human-ENCSR844RVX-rep1.1x25mers.chrM.unique
zcat K562-EFTUD2-human-ENCSR844RVX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2-human-ENCSR844RVX-rep2.1x25mers.chrM.unique
zcat K562-EFTUD2_eCLIP_mock_input-human-ENCSR266UVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EFTUD2_eCLIP_mock_input-human-ENCSR266UVO-rep1.1x25mers.chrM.unique
zcat K562-EIF4G2-human-ENCSR307YIW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2-human-ENCSR307YIW-rep1.1x25mers.chrM.unique
zcat K562-EIF4G2-human-ENCSR307YIW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2-human-ENCSR307YIW-rep2.1x25mers.chrM.unique
zcat K562-EIF4G2_eCLIP_mock_input-human-ENCSR651NUF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EIF4G2_eCLIP_mock_input-human-ENCSR651NUF-rep1.1x25mers.chrM.unique
zcat K562-EWSR1-human-ENCSR887LPK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1-human-ENCSR887LPK-rep1.1x25mers.chrM.unique
zcat K562-EWSR1-human-ENCSR887LPK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1-human-ENCSR887LPK-rep2.1x25mers.chrM.unique
zcat K562-EWSR1_eCLIP_mock_input-human-ENCSR067UKU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EWSR1_eCLIP_mock_input-human-ENCSR067UKU-rep1.1x25mers.chrM.unique
zcat K562-EXOSC5-human-ENCSR013CTQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5-human-ENCSR013CTQ-rep1.1x25mers.chrM.unique
zcat K562-EXOSC5-human-ENCSR013CTQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5-human-ENCSR013CTQ-rep2.1x25mers.chrM.unique
zcat K562-EXOSC5_eCLIP_mock_input-human-ENCSR308RMD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-EXOSC5_eCLIP_mock_input-human-ENCSR308RMD-rep1.1x25mers.chrM.unique
zcat K562-FAM120A-human-ENCSR006OEQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A-human-ENCSR006OEQ-rep1.1x25mers.chrM.unique
zcat K562-FAM120A-human-ENCSR006OEQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A-human-ENCSR006OEQ-rep2.1x25mers.chrM.unique
zcat K562-FAM120A_eCLIP_mock_input-human-ENCSR811FFO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FAM120A_eCLIP_mock_input-human-ENCSR811FFO-rep1.1x25mers.chrM.unique
zcat K562-FASTKD2-human-ENCSR887FHF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2-human-ENCSR887FHF-rep1.1x25mers.chrM.unique
zcat K562-FASTKD2-human-ENCSR887FHF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2-human-ENCSR887FHF-rep2.1x25mers.chrM.unique
zcat K562-FASTKD2_eCLIP_mock_input-human-ENCSR119AFY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FASTKD2_eCLIP_mock_input-human-ENCSR119AFY-rep1.1x25mers.chrM.unique
zcat K562-FMR1-human-ENCSR331VNX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1-human-ENCSR331VNX-rep1.1x25mers.chrM.unique
zcat K562-FMR1-human-ENCSR331VNX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1-human-ENCSR331VNX-rep2.1x25mers.chrM.unique
zcat K562-FMR1_eCLIP_mock_input-human-ENCSR735MBZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FMR1_eCLIP_mock_input-human-ENCSR735MBZ-rep1.1x25mers.chrM.unique
zcat K562-FTO-human-ENCSR989SMC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO-human-ENCSR989SMC-rep1.1x25mers.chrM.unique
zcat K562-FTO-human-ENCSR989SMC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO-human-ENCSR989SMC-rep2.1x25mers.chrM.unique
zcat K562-FTO_eCLIP_mock_input-human-ENCSR575DKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FTO_eCLIP_mock_input-human-ENCSR575DKE-rep1.1x25mers.chrM.unique
zcat K562-FXR1-human-ENCSR774RFN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1-human-ENCSR774RFN-rep1.1x25mers.chrM.unique
zcat K562-FXR1-human-ENCSR774RFN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1-human-ENCSR774RFN-rep2.1x25mers.chrM.unique
zcat K562-FXR1_eCLIP_mock_input-human-ENCSR562BJW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR1_eCLIP_mock_input-human-ENCSR562BJW-rep1.1x25mers.chrM.unique
zcat K562-FXR2-human-ENCSR224QWC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2-human-ENCSR224QWC-rep1.1x25mers.chrM.unique
zcat K562-FXR2-human-ENCSR224QWC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2-human-ENCSR224QWC-rep2.1x25mers.chrM.unique
zcat K562-FXR2_eCLIP_mock_input-human-ENCSR411IMJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-FXR2_eCLIP_mock_input-human-ENCSR411IMJ-rep1.1x25mers.chrM.unique
zcat K562-GEMIN5-human-ENCSR238CLX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5-human-ENCSR238CLX-rep1.1x25mers.chrM.unique
zcat K562-GEMIN5-human-ENCSR238CLX-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5-human-ENCSR238CLX-rep2.1x25mers.chrM.unique
zcat K562-GEMIN5_eCLIP_mock_input-human-ENCSR347MVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GEMIN5_eCLIP_mock_input-human-ENCSR347MVO-rep1.1x25mers.chrM.unique
zcat K562-GNL3-human-ENCSR301UQM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3-human-ENCSR301UQM-rep1.1x25mers.chrM.unique
zcat K562-GNL3-human-ENCSR301UQM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3-human-ENCSR301UQM-rep2.1x25mers.chrM.unique
zcat K562-GNL3_eCLIP_mock_input-human-ENCSR977GTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GNL3_eCLIP_mock_input-human-ENCSR977GTT-rep1.1x25mers.chrM.unique
zcat K562-GPKOW-human-ENCSR647CLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW-human-ENCSR647CLF-rep1.1x25mers.chrM.unique
zcat K562-GPKOW-human-ENCSR647CLF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW-human-ENCSR647CLF-rep2.1x25mers.chrM.unique
zcat K562-GPKOW_eCLIP_mock_input-human-ENCSR393STP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GPKOW_eCLIP_mock_input-human-ENCSR393STP-rep1.1x25mers.chrM.unique
zcat K562-GTF2F1-human-ENCSR736AAG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1-human-ENCSR736AAG-rep1.1x25mers.chrM.unique
zcat K562-GTF2F1-human-ENCSR736AAG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1-human-ENCSR736AAG-rep2.1x25mers.chrM.unique
zcat K562-GTF2F1_eCLIP_mock_input-human-ENCSR157BRV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-GTF2F1_eCLIP_mock_input-human-ENCSR157BRV-rep1.1x25mers.chrM.unique
zcat K562-HLTF-human-ENCSR589YHM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF-human-ENCSR589YHM-rep1.1x25mers.chrM.unique
zcat K562-HLTF-human-ENCSR589YHM-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF-human-ENCSR589YHM-rep2.1x25mers.chrM.unique
zcat K562-HLTF_eCLIP_mock_input-human-ENCSR502NKG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HLTF_eCLIP_mock_input-human-ENCSR502NKG-rep1.1x25mers.chrM.unique
zcat K562-HNRNPA1-human-ENCSR154HRN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1-human-ENCSR154HRN-rep1.1x25mers.chrM.unique
zcat K562-HNRNPA1-human-ENCSR154HRN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1-human-ENCSR154HRN-rep2.1x25mers.chrM.unique
zcat K562-HNRNPA1_eCLIP_mock_input-human-ENCSR898ZCL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPA1_eCLIP_mock_input-human-ENCSR898ZCL-rep1.1x25mers.chrM.unique
zcat K562-HNRNPK-human-ENCSR268ETU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK-human-ENCSR268ETU-rep1.1x25mers.chrM.unique
zcat K562-HNRNPK-human-ENCSR268ETU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK-human-ENCSR268ETU-rep2.1x25mers.chrM.unique
zcat K562-HNRNPK_eCLIP_mock_input-human-ENCSR669DKA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPK_eCLIP_mock_input-human-ENCSR669DKA-rep1.1x25mers.chrM.unique
zcat K562-HNRNPL-human-ENCSR795CAI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL-human-ENCSR795CAI-rep1.1x25mers.chrM.unique
zcat K562-HNRNPL-human-ENCSR795CAI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL-human-ENCSR795CAI-rep2.1x25mers.chrM.unique
zcat K562-HNRNPL_eCLIP_mock_input-human-ENCSR299AAB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPL_eCLIP_mock_input-human-ENCSR299AAB-rep1.1x25mers.chrM.unique
zcat K562-HNRNPM-human-ENCSR412NOW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM-human-ENCSR412NOW-rep1.1x25mers.chrM.unique
zcat K562-HNRNPM-human-ENCSR412NOW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM-human-ENCSR412NOW-rep2.1x25mers.chrM.unique
zcat K562-HNRNPM_eCLIP_mock_input-human-ENCSR212ILN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPM_eCLIP_mock_input-human-ENCSR212ILN-rep1.1x25mers.chrM.unique
zcat K562-HNRNPU-human-ENCSR520BZQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU-human-ENCSR520BZQ-rep1.1x25mers.chrM.unique
zcat K562-HNRNPU-human-ENCSR520BZQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU-human-ENCSR520BZQ-rep2.1x25mers.chrM.unique
zcat K562-HNRNPUL1-human-ENCSR571VHI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1-human-ENCSR571VHI-rep1.1x25mers.chrM.unique
zcat K562-HNRNPUL1-human-ENCSR571VHI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1-human-ENCSR571VHI-rep2.1x25mers.chrM.unique
zcat K562-HNRNPUL1_eCLIP_mock_input-human-ENCSR482AWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPUL1_eCLIP_mock_input-human-ENCSR482AWB-rep1.1x25mers.chrM.unique
zcat K562-HNRNPU_eCLIP_mock_input-human-ENCSR829SLO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-HNRNPU_eCLIP_mock_input-human-ENCSR829SLO-rep1.1x25mers.chrM.unique
zcat K562-IGF2BP1-human-ENCSR975KIR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1-human-ENCSR975KIR-rep1.1x25mers.chrM.unique
zcat K562-IGF2BP1-human-ENCSR975KIR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1-human-ENCSR975KIR-rep2.1x25mers.chrM.unique
zcat K562-IGF2BP1_eCLIP_mock_input-human-ENCSR125CLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP1_eCLIP_mock_input-human-ENCSR125CLF-rep1.1x25mers.chrM.unique
zcat K562-IGF2BP2-human-ENCSR062NNB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2-human-ENCSR062NNB-rep1.1x25mers.chrM.unique
zcat K562-IGF2BP2-human-ENCSR062NNB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2-human-ENCSR062NNB-rep2.1x25mers.chrM.unique
zcat K562-IGF2BP2_eCLIP_mock_input-human-ENCSR387RGT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-IGF2BP2_eCLIP_mock_input-human-ENCSR387RGT-rep1.1x25mers.chrM.unique
zcat K562-ILF3-human-ENCSR438KWZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3-human-ENCSR438KWZ-rep1.1x25mers.chrM.unique
zcat K562-ILF3-human-ENCSR438KWZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3-human-ENCSR438KWZ-rep2.1x25mers.chrM.unique
zcat K562-ILF3_eCLIP_mock_input-human-ENCSR760SFB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ILF3_eCLIP_mock_input-human-ENCSR760SFB-rep1.1x25mers.chrM.unique
zcat K562-KHDRBS1-human-ENCSR628IDK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1-human-ENCSR628IDK-rep1.1x25mers.chrM.unique
zcat K562-KHDRBS1-human-ENCSR628IDK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1-human-ENCSR628IDK-rep2.1x25mers.chrM.unique
zcat K562-KHDRBS1_eCLIP_mock_input-human-ENCSR197NFH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHDRBS1_eCLIP_mock_input-human-ENCSR197NFH-rep1.1x25mers.chrM.unique
zcat K562-KHSRP-human-ENCSR438GZQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP-human-ENCSR438GZQ-rep1.1x25mers.chrM.unique
zcat K562-KHSRP-human-ENCSR438GZQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP-human-ENCSR438GZQ-rep2.1x25mers.chrM.unique
zcat K562-KHSRP_eCLIP_mock_input-human-ENCSR305IPT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-KHSRP_eCLIP_mock_input-human-ENCSR305IPT-rep1.1x25mers.chrM.unique
zcat K562-LARP4-human-ENCSR888YTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4-human-ENCSR888YTT-rep1.1x25mers.chrM.unique
zcat K562-LARP4-human-ENCSR888YTT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4-human-ENCSR888YTT-rep2.1x25mers.chrM.unique
zcat K562-LARP4_eCLIP_mock_input-human-ENCSR679NKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP4_eCLIP_mock_input-human-ENCSR679NKE-rep1.1x25mers.chrM.unique
zcat K562-LARP7-human-ENCSR456KXI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7-human-ENCSR456KXI-rep1.1x25mers.chrM.unique
zcat K562-LARP7-human-ENCSR456KXI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7-human-ENCSR456KXI-rep2.1x25mers.chrM.unique
zcat K562-LARP7_eCLIP_mock_input-human-ENCSR863ZGZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LARP7_eCLIP_mock_input-human-ENCSR863ZGZ-rep1.1x25mers.chrM.unique
zcat K562-LIN28B-human-ENCSR970NKP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B-human-ENCSR970NKP-rep1.1x25mers.chrM.unique
zcat K562-LIN28B-human-ENCSR970NKP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B-human-ENCSR970NKP-rep2.1x25mers.chrM.unique
zcat K562-LIN28B_eCLIP_mock_input-human-ENCSR399CBP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LIN28B_eCLIP_mock_input-human-ENCSR399CBP-rep1.1x25mers.chrM.unique
zcat K562-LSM11-human-ENCSR022BVV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11-human-ENCSR022BVV-rep1.1x25mers.chrM.unique
zcat K562-LSM11-human-ENCSR022BVV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11-human-ENCSR022BVV-rep2.1x25mers.chrM.unique
zcat K562-LSM11_eCLIP_mock_input-human-ENCSR952UOL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-LSM11_eCLIP_mock_input-human-ENCSR952UOL-rep1.1x25mers.chrM.unique
zcat K562-METAP2-human-ENCSR303OQD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2-human-ENCSR303OQD-rep1.1x25mers.chrM.unique
zcat K562-METAP2-human-ENCSR303OQD-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2-human-ENCSR303OQD-rep2.1x25mers.chrM.unique
zcat K562-METAP2_eCLIP_mock_input-human-ENCSR750NTM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-METAP2_eCLIP_mock_input-human-ENCSR750NTM-rep1.1x25mers.chrM.unique
zcat K562-MTPAP-human-ENCSR200DKE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP-human-ENCSR200DKE-rep1.1x25mers.chrM.unique
zcat K562-MTPAP-human-ENCSR200DKE-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP-human-ENCSR200DKE-rep2.1x25mers.chrM.unique
zcat K562-MTPAP_eCLIP_mock_input-human-ENCSR927XDB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-MTPAP_eCLIP_mock_input-human-ENCSR927XDB-rep1.1x25mers.chrM.unique
zcat K562-NCBP2-human-ENCSR484LTQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2-human-ENCSR484LTQ-rep1.1x25mers.chrM.unique
zcat K562-NCBP2-human-ENCSR484LTQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2-human-ENCSR484LTQ-rep2.1x25mers.chrM.unique
zcat K562-NCBP2_eCLIP_mock_input-human-ENCSR921SHJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NCBP2_eCLIP_mock_input-human-ENCSR921SHJ-rep1.1x25mers.chrM.unique
zcat K562-NFX1_eCLIP_mock_input-human-ENCSR821ESG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NFX1_eCLIP_mock_input-human-ENCSR821ESG-rep1.1x25mers.chrM.unique
zcat K562-NOLC1-human-ENCSR001VAC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1-human-ENCSR001VAC-rep1.1x25mers.chrM.unique
zcat K562-NOLC1-human-ENCSR001VAC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1-human-ENCSR001VAC-rep2.1x25mers.chrM.unique
zcat K562-NOLC1_eCLIP_mock_input-human-ENCSR009CIV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NOLC1_eCLIP_mock_input-human-ENCSR009CIV-rep1.1x25mers.chrM.unique
zcat K562-NONO-human-ENCSR861PAR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO-human-ENCSR861PAR-rep1.1x25mers.chrM.unique
zcat K562-NONO-human-ENCSR861PAR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO-human-ENCSR861PAR-rep2.1x25mers.chrM.unique
zcat K562-NONO__eCLIP_mock_input-human-ENCSR487EUV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NONO__eCLIP_mock_input-human-ENCSR487EUV-rep1.1x25mers.chrM.unique
zcat K562-NPM1-human-ENCSR867DSZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1-human-ENCSR867DSZ-rep1.1x25mers.chrM.unique
zcat K562-NPM1-human-ENCSR867DSZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1-human-ENCSR867DSZ-rep2.1x25mers.chrM.unique
zcat K562-NPM1_eCLIP_mock_input-human-ENCSR468ZQA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NPM1_eCLIP_mock_input-human-ENCSR468ZQA-rep1.1x25mers.chrM.unique
zcat K562-NSUN2-human-ENCSR081JYH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2-human-ENCSR081JYH-rep1.1x25mers.chrM.unique
zcat K562-NSUN2-human-ENCSR081JYH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2-human-ENCSR081JYH-rep2.1x25mers.chrM.unique
zcat K562-NSUN2_eCLIP_mock_input-human-ENCSR595PFU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-NSUN2_eCLIP_mock_input-human-ENCSR595PFU-rep1.1x25mers.chrM.unique
zcat K562-POLR2G_eCLIP_mock_input-human-ENCSR585TQT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-POLR2G_eCLIP_mock_input-human-ENCSR585TQT-rep1.1x25mers.chrM.unique
zcat K562-PPIL4-human-ENCSR197INS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4-human-ENCSR197INS-rep1.1x25mers.chrM.unique
zcat K562-PPIL4-human-ENCSR197INS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4-human-ENCSR197INS-rep2.1x25mers.chrM.unique
zcat K562-PPIL4_eCLIP_mock_input-human-ENCSR346IHS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PPIL4_eCLIP_mock_input-human-ENCSR346IHS-rep1.1x25mers.chrM.unique
zcat K562-PRPF8-human-ENCSR534YOI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8-human-ENCSR534YOI-rep1.1x25mers.chrM.unique
zcat K562-PRPF8-human-ENCSR534YOI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8-human-ENCSR534YOI-rep2.1x25mers.chrM.unique
zcat K562-PRPF8_eCLIP_mock_input-human-ENCSR096SZE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PRPF8_eCLIP_mock_input-human-ENCSR096SZE-rep1.1x25mers.chrM.unique
zcat K562-PTBP1-human-ENCSR981WKN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1-human-ENCSR981WKN-rep1.1x25mers.chrM.unique
zcat K562-PTBP1-human-ENCSR981WKN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1-human-ENCSR981WKN-rep2.1x25mers.chrM.unique
zcat K562-PTBP1_eCLIP_mock_input-human-ENCSR445FZX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PTBP1_eCLIP_mock_input-human-ENCSR445FZX-rep1.1x25mers.chrM.unique
zcat K562-PUM2-human-ENCSR661ICQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2-human-ENCSR661ICQ-rep1.1x25mers.chrM.unique
zcat K562-PUM2-human-ENCSR661ICQ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2-human-ENCSR661ICQ-rep2.1x25mers.chrM.unique
zcat K562-PUM2_eCLIP_mock_input-human-ENCSR439GXW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUM2_eCLIP_mock_input-human-ENCSR439GXW-rep1.1x25mers.chrM.unique
zcat K562-PUS1-human-ENCSR291XPT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1-human-ENCSR291XPT-rep1.1x25mers.chrM.unique
zcat K562-PUS1-human-ENCSR291XPT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1-human-ENCSR291XPT-rep2.1x25mers.chrM.unique
zcat K562-PUS1_eCLIP_mock_input-human-ENCSR869TOB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-PUS1_eCLIP_mock_input-human-ENCSR869TOB-rep1.1x25mers.chrM.unique
zcat K562-QKI-human-ENCSR366YOG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI-human-ENCSR366YOG-rep1.1x25mers.chrM.unique
zcat K562-QKI-human-ENCSR366YOG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI-human-ENCSR366YOG-rep2.1x25mers.chrM.unique
zcat K562-QKI_eCLIP_mock_input-human-ENCSR615AAW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-QKI_eCLIP_mock_input-human-ENCSR615AAW-rep1.1x25mers.chrM.unique
zcat K562-RBFOX2-human-ENCSR756CKJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2-human-ENCSR756CKJ-rep1.1x25mers.chrM.unique
zcat K562-RBFOX2-human-ENCSR756CKJ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2-human-ENCSR756CKJ-rep2.1x25mers.chrM.unique
zcat K562-RBFOX2_eCLIP_mock_input-human-ENCSR051IXX-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBFOX2_eCLIP_mock_input-human-ENCSR051IXX-rep1.1x25mers.chrM.unique
zcat K562-RBM15-human-ENCSR196INN-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15-human-ENCSR196INN-rep1.1x25mers.chrM.unique
zcat K562-RBM15-human-ENCSR196INN-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15-human-ENCSR196INN-rep2.1x25mers.chrM.unique
zcat K562-RBM15_eCLIP_mock_input-human-ENCSR454EER-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM15_eCLIP_mock_input-human-ENCSR454EER-rep1.1x25mers.chrM.unique
zcat K562-RBM22-human-ENCSR295OKT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22-human-ENCSR295OKT-rep1.1x25mers.chrM.unique
zcat K562-RBM22-human-ENCSR295OKT-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22-human-ENCSR295OKT-rep2.1x25mers.chrM.unique
zcat K562-RBM22_eCLIP_mock_input-human-ENCSR344EGD-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RBM22_eCLIP_mock_input-human-ENCSR344EGD-rep1.1x25mers.chrM.unique
zcat K562-RPS11-human-ENCSR269AJF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11-human-ENCSR269AJF-rep1.1x25mers.chrM.unique
zcat K562-RPS11-human-ENCSR269AJF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11-human-ENCSR269AJF-rep2.1x25mers.chrM.unique
zcat K562-RPS11_eCLIP_mock_input-human-ENCSR881RJL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS11_eCLIP_mock_input-human-ENCSR881RJL-rep1.1x25mers.chrM.unique
zcat K562-RPS24_eCLIP_mock_input-human-ENCSR567ZND-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS24_eCLIP_mock_input-human-ENCSR567ZND-rep1.1x25mers.chrM.unique
zcat K562-RPS3-human-ENCSR120EAR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3-human-ENCSR120EAR-rep1.1x25mers.chrM.unique
zcat K562-RPS3-human-ENCSR120EAR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3-human-ENCSR120EAR-rep2.1x25mers.chrM.unique
zcat K562-RPS3_eCLIP_mock_input-human-ENCSR494JFR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS3_eCLIP_mock_input-human-ENCSR494JFR-rep1.1x25mers.chrM.unique
zcat K562-RPS5_eCLIP_mock_input-human-ENCSR486QAE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-RPS5_eCLIP_mock_input-human-ENCSR486QAE-rep1.1x25mers.chrM.unique
zcat K562-SAFB2-human-ENCSR943MHU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2-human-ENCSR943MHU-rep1.1x25mers.chrM.unique
zcat K562-SAFB2-human-ENCSR943MHU-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2-human-ENCSR943MHU-rep2.1x25mers.chrM.unique
zcat K562-SAFB2_eCLIP_mock_input-human-ENCSR978JXM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SAFB2_eCLIP_mock_input-human-ENCSR978JXM-rep1.1x25mers.chrM.unique
zcat K562-SBDS-human-ENCSR059CWF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS-human-ENCSR059CWF-rep1.1x25mers.chrM.unique
zcat K562-SBDS-human-ENCSR059CWF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS-human-ENCSR059CWF-rep2.1x25mers.chrM.unique
zcat K562-SBDS_eCLIP_mock_input-human-ENCSR038TMA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SBDS_eCLIP_mock_input-human-ENCSR038TMA-rep1.1x25mers.chrM.unique
zcat K562-SERBP1-human-ENCSR121GQH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1-human-ENCSR121GQH-rep1.1x25mers.chrM.unique
zcat K562-SERBP1-human-ENCSR121GQH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1-human-ENCSR121GQH-rep2.1x25mers.chrM.unique
zcat K562-SERBP1_eCLIP_mock_input-human-ENCSR752YLF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SERBP1_eCLIP_mock_input-human-ENCSR752YLF-rep1.1x25mers.chrM.unique
zcat K562-SF3B1-human-ENCSR133QEA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1-human-ENCSR133QEA-rep1.1x25mers.chrM.unique
zcat K562-SF3B1-human-ENCSR133QEA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1-human-ENCSR133QEA-rep2.1x25mers.chrM.unique
zcat K562-SF3B1_eCLIP_mock_input-human-ENCSR496UBM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B1_eCLIP_mock_input-human-ENCSR496UBM-rep1.1x25mers.chrM.unique
zcat K562-SF3B4-human-ENCSR267OLV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4-human-ENCSR267OLV-rep1.1x25mers.chrM.unique
zcat K562-SF3B4-human-ENCSR267OLV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4-human-ENCSR267OLV-rep2.1x25mers.chrM.unique
zcat K562-SF3B4_eCLIP_mock_input-human-ENCSR305KNE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SF3B4_eCLIP_mock_input-human-ENCSR305KNE-rep1.1x25mers.chrM.unique
zcat K562-SLBP-human-ENCSR483NOP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP-human-ENCSR483NOP-rep1.1x25mers.chrM.unique
zcat K562-SLBP-human-ENCSR483NOP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP-human-ENCSR483NOP-rep2.1x25mers.chrM.unique
zcat K562-SLBP_eCLIP_mock_input-human-ENCSR950WBG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLBP_eCLIP_mock_input-human-ENCSR950WBG-rep1.1x25mers.chrM.unique
zcat K562-SLTM-human-ENCSR000SSH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM-human-ENCSR000SSH-rep1.1x25mers.chrM.unique
zcat K562-SLTM-human-ENCSR000SSH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM-human-ENCSR000SSH-rep2.1x25mers.chrM.unique
zcat K562-SLTM_eCLIP_mock_input-human-ENCSR820GBM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SLTM_eCLIP_mock_input-human-ENCSR820GBM-rep1.1x25mers.chrM.unique
zcat K562-SMNDC1-human-ENCSR658IQB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1-human-ENCSR658IQB-rep1.1x25mers.chrM.unique
zcat K562-SMNDC1-human-ENCSR658IQB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1-human-ENCSR658IQB-rep2.1x25mers.chrM.unique
zcat K562-SMNDC1_eCLIP_mock_input-human-ENCSR631CJA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SMNDC1_eCLIP_mock_input-human-ENCSR631CJA-rep1.1x25mers.chrM.unique
zcat K562-SND1-human-ENCSR128VXC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1-human-ENCSR128VXC-rep1.1x25mers.chrM.unique
zcat K562-SND1-human-ENCSR128VXC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1-human-ENCSR128VXC-rep2.1x25mers.chrM.unique
zcat K562-SND1_eCLIP_mock_input-human-ENCSR435EVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SND1_eCLIP_mock_input-human-ENCSR435EVK-rep1.1x25mers.chrM.unique
zcat K562-SRSF1-human-ENCSR432XUP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1-human-ENCSR432XUP-rep1.1x25mers.chrM.unique
zcat K562-SRSF1-human-ENCSR432XUP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1-human-ENCSR432XUP-rep2.1x25mers.chrM.unique
zcat K562-SRSF1_eCLIP_mock_input-human-ENCSR925TYQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF1_eCLIP_mock_input-human-ENCSR925TYQ-rep1.1x25mers.chrM.unique
zcat K562-SRSF7-human-ENCSR468FSW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7-human-ENCSR468FSW-rep1.1x25mers.chrM.unique
zcat K562-SRSF7-human-ENCSR468FSW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7-human-ENCSR468FSW-rep2.1x25mers.chrM.unique
zcat K562-SRSF7_eCLIP_mock_input-human-ENCSR145PHJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-SRSF7_eCLIP_mock_input-human-ENCSR145PHJ-rep1.1x25mers.chrM.unique
zcat K562-TAF15-human-ENCSR568DZW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15-human-ENCSR568DZW-rep1.1x25mers.chrM.unique
zcat K562-TAF15-human-ENCSR568DZW-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15-human-ENCSR568DZW-rep2.1x25mers.chrM.unique
zcat K562-TAF15_eCLIP_mock_input-human-ENCSR653CNZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TAF15_eCLIP_mock_input-human-ENCSR653CNZ-rep1.1x25mers.chrM.unique
zcat K562-TARDBP-human-ENCSR584TCR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP-human-ENCSR584TCR-rep1.1x25mers.chrM.unique
zcat K562-TARDBP-human-ENCSR584TCR-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP-human-ENCSR584TCR-rep2.1x25mers.chrM.unique
zcat K562-TARDBP_eCLIP_mock_input-human-ENCSR924OLO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TARDBP_eCLIP_mock_input-human-ENCSR924OLO-rep1.1x25mers.chrM.unique
zcat K562-TBRG4-human-ENCSR506OTC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4-human-ENCSR506OTC-rep1.1x25mers.chrM.unique
zcat K562-TBRG4-human-ENCSR506OTC-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4-human-ENCSR506OTC-rep2.1x25mers.chrM.unique
zcat K562-TBRG4_eCLIP_mock_input-human-ENCSR512EZA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TBRG4_eCLIP_mock_input-human-ENCSR512EZA-rep1.1x25mers.chrM.unique
zcat K562-TIA1-human-ENCSR057DWB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1-human-ENCSR057DWB-rep1.1x25mers.chrM.unique
zcat K562-TIA1-human-ENCSR057DWB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1-human-ENCSR057DWB-rep2.1x25mers.chrM.unique
zcat K562-TIA1_eCLIP_mock_input-human-ENCSR356GCJ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TIA1_eCLIP_mock_input-human-ENCSR356GCJ-rep1.1x25mers.chrM.unique
zcat K562-TNRC6A_eCLIP_mock_input-human-ENCSR800LOQ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TNRC6A_eCLIP_mock_input-human-ENCSR800LOQ-rep1.1x25mers.chrM.unique
zcat K562-TRA2A-human-ENCSR365NVO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A-human-ENCSR365NVO-rep1.1x25mers.chrM.unique
zcat K562-TRA2A-human-ENCSR365NVO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A-human-ENCSR365NVO-rep2.1x25mers.chrM.unique
zcat K562-TRA2A_eCLIP_mock_input-human-ENCSR619RLC-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TRA2A_eCLIP_mock_input-human-ENCSR619RLC-rep1.1x25mers.chrM.unique
zcat K562-TROVE2-human-ENCSR539ZTS-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2-human-ENCSR539ZTS-rep1.1x25mers.chrM.unique
zcat K562-TROVE2-human-ENCSR539ZTS-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2-human-ENCSR539ZTS-rep2.1x25mers.chrM.unique
zcat K562-TROVE2_eCLIP_mock_input-human-ENCSR687GJH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-TROVE2_eCLIP_mock_input-human-ENCSR687GJH-rep1.1x25mers.chrM.unique
zcat K562-U2AF1-human-ENCSR862QCH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1-human-ENCSR862QCH-rep1.1x25mers.chrM.unique
zcat K562-U2AF1-human-ENCSR862QCH-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1-human-ENCSR862QCH-rep2.1x25mers.chrM.unique
zcat K562-U2AF1_eCLIP_mock_input-human-ENCSR482ZSE-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF1_eCLIP_mock_input-human-ENCSR482ZSE-rep1.1x25mers.chrM.unique
zcat K562-U2AF2-human-ENCSR893RAV-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2-human-ENCSR893RAV-rep1.1x25mers.chrM.unique
zcat K562-U2AF2-human-ENCSR893RAV-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2-human-ENCSR893RAV-rep2.1x25mers.chrM.unique
zcat K562-U2AF2_eCLIP_mock_input-human-ENCSR871RTL-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-U2AF2_eCLIP_mock_input-human-ENCSR871RTL-rep1.1x25mers.chrM.unique
zcat K562-UCHL5-human-ENCSR349KMG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5-human-ENCSR349KMG-rep1.1x25mers.chrM.unique
zcat K562-UCHL5-human-ENCSR349KMG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5-human-ENCSR349KMG-rep2.1x25mers.chrM.unique
zcat K562-UCHL5_eCLIP_mock_input-human-ENCSR751CSY-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UCHL5_eCLIP_mock_input-human-ENCSR751CSY-rep1.1x25mers.chrM.unique
zcat K562-UPF1-human-ENCSR456ASB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1-human-ENCSR456ASB-rep1.1x25mers.chrM.unique
zcat K562-UPF1-human-ENCSR456ASB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1-human-ENCSR456ASB-rep2.1x25mers.chrM.unique
zcat K562-UPF1_eCLIP_mock_input-human-ENCSR461LGW-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-UPF1_eCLIP_mock_input-human-ENCSR461LGW-rep1.1x25mers.chrM.unique
zcat K562-XRCC6-human-ENCSR258QKO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6-human-ENCSR258QKO-rep1.1x25mers.chrM.unique
zcat K562-XRCC6-human-ENCSR258QKO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6-human-ENCSR258QKO-rep2.1x25mers.chrM.unique
zcat K562-XRCC6_eCLIP_mock_input-human-ENCSR687HHB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRCC6_eCLIP_mock_input-human-ENCSR687HHB-rep1.1x25mers.chrM.unique
zcat K562-XRN2-human-ENCSR657TZB-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2-human-ENCSR657TZB-rep1.1x25mers.chrM.unique
zcat K562-XRN2-human-ENCSR657TZB-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2-human-ENCSR657TZB-rep2.1x25mers.chrM.unique
zcat K562-XRN2_eCLIP_mock_input-human-ENCSR170XQH-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-XRN2_eCLIP_mock_input-human-ENCSR170XQH-rep1.1x25mers.chrM.unique
zcat K562-YBX3-human-ENCSR529FKI-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3-human-ENCSR529FKI-rep1.1x25mers.chrM.unique
zcat K562-YBX3-human-ENCSR529FKI-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3-human-ENCSR529FKI-rep2.1x25mers.chrM.unique
zcat K562-YBX3_eCLIP_mock_input-human-ENCSR660VTT-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YBX3_eCLIP_mock_input-human-ENCSR660VTT-rep1.1x25mers.chrM.unique
zcat K562-YWHAG-human-ENCSR867ZVK-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG-human-ENCSR867ZVK-rep1.1x25mers.chrM.unique
zcat K562-YWHAG-human-ENCSR867ZVK-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG-human-ENCSR867ZVK-rep2.1x25mers.chrM.unique
zcat K562-YWHAG_eCLIP_mock_input-human-ENCSR812PBU-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-YWHAG_eCLIP_mock_input-human-ENCSR812PBU-rep1.1x25mers.chrM.unique
zcat K562-ZC3H11A-human-ENCSR712IAG-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A-human-ENCSR712IAG-rep1.1x25mers.chrM.unique
zcat K562-ZC3H11A-human-ENCSR712IAG-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A-human-ENCSR712IAG-rep2.1x25mers.chrM.unique
zcat K562-ZC3H11A_eCLIP_mock_input-human-ENCSR321GBR-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZC3H11A_eCLIP_mock_input-human-ENCSR321GBR-rep1.1x25mers.chrM.unique
zcat K562-ZNF622-human-ENCSR657TZZ-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622-human-ENCSR657TZZ-rep1.1x25mers.chrM.unique
zcat K562-ZNF622-human-ENCSR657TZZ-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622-human-ENCSR657TZZ-rep2.1x25mers.chrM.unique
zcat K562-ZNF622_eCLIP_mock_input-human-ENCSR594RFP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZNF622_eCLIP_mock_input-human-ENCSR594RFP-rep1.1x25mers.chrM.unique
zcat K562-ZRANB2-human-ENCSR663NRA-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2-human-ENCSR663NRA-rep1.1x25mers.chrM.unique
zcat K562-ZRANB2-human-ENCSR663NRA-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2-human-ENCSR663NRA-rep2.1x25mers.chrM.unique
zcat K562-ZRANB2_eCLIP_mock_input-human-ENCSR528HOM-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - K562-ZRANB2_eCLIP_mock_input-human-ENCSR528HOM-rep1.1x25mers.chrM.unique
zcat adrenal_gland-DGCR8-human-ENCSR634MFO-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8-human-ENCSR634MFO-rep1.1x25mers.chrM.unique
zcat adrenal_gland-DGCR8-human-ENCSR634MFO-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8-human-ENCSR634MFO-rep2.1x25mers.chrM.unique
zcat adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep1.1x25mers.chrM.unique
zcat adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-DGCR8_eCLIP_mock_input-human-ENCSR217SVF-rep2.1x25mers.chrM.unique
zcat adrenal_gland-HNRNPU-human-ENCSR368GER-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU-human-ENCSR368GER-rep1.1x25mers.chrM.unique
zcat adrenal_gland-HNRNPU-human-ENCSR368GER-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU-human-ENCSR368GER-rep2.1x25mers.chrM.unique
zcat adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep1*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep1.1x25mers.chrM.unique
zcat adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep2*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 25 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 8 -v 0 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - adrenal_gland-HNRNPU_eCLIP_mock_input-human-ENCSR096YAP-rep2.1x25mers.chrM.unique