zcat FGFR1_LIF-GSM1603268/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_LIF-GSM1603268.1x50mers.chrM.unique
zcat RXRa_LIF-GSM1603269/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RXRa_LIF-GSM1603269.1x50mers.chrM.unique
zcat Nur77_LIF-GSM1603270/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Nur77_LIF-GSM1603270.1x50mers.chrM.unique
zcat FGFR1_RA-GSM1603271/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_RA-GSM1603271.1x50mers.chrM.unique
zcat RXRa_RA-GSM1603272/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RXRa_RA-GSM1603272.1x50mers.chrM.unique
zcat Nur77_RA-GSM1603273/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Nur77_RA-GSM1603273.1x50mers.chrM.unique
zcat H3.3_RA-GSM1603274/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H3.3_RA-GSM1603274.1x50mers.chrM.unique
zcat FGFR1_RA_Exp2-GSM1603275/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_RA_Exp2-GSM1603275.1x50mers.chrM.unique
zcat FGFR1_LIF-GSM1603268/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_LIF-GSM1603268.1x50mers.mm10.unique
zcat RXRa_LIF-GSM1603269/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RXRa_LIF-GSM1603269.1x50mers.mm10.unique
zcat Nur77_LIF-GSM1603270/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Nur77_LIF-GSM1603270.1x50mers.mm10.unique
zcat FGFR1_RA-GSM1603271/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_RA-GSM1603271.1x50mers.mm10.unique
zcat RXRa_RA-GSM1603272/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - RXRa_RA-GSM1603272.1x50mers.mm10.unique
zcat Nur77_RA-GSM1603273/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Nur77_RA-GSM1603273.1x50mers.mm10.unique
zcat H3.3_RA-GSM1603274/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - H3.3_RA-GSM1603274.1x50mers.mm10.unique
zcat FGFR1_RA_Exp2-GSM1603275/*.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10 -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bowtie-indexes/mm10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - FGFR1_RA_Exp2-GSM1603275.1x50mers.mm10.unique