/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-0h-a_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-0h-b_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-24h-a_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-24h-b_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-24hI-a_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-24hI-b_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-6h-a_R1.2x36mers.hg19-male.nochrM.bam &
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view 2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.hg19-male.bam | egrep -v chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa - -o 2017-07-17-FrozKera-DMSO-6h-b_R1.2x36mers.hg19-male.nochrM.bam &