/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam | egrep -v 'sacCer3_chrM|Candida_glabrata_mito|Schizosaccharomyces_pombe_chrM|Schizosaccharomyces_pombe_MTRSchizosaccharomyces_pombe_AB325691' | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o L1979-210117L05_GM16_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam | egrep -v 'sacCer3_chrM|Candida_glabrata_mito|Schizosaccharomyces_pombe_chrM|Schizosaccharomyces_pombe_MTRSchizosaccharomyces_pombe_AB325691' | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o L1980-210117L06_GM17_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam | egrep -v 'sacCer3_chrM|Candida_glabrata_mito|Schizosaccharomyces_pombe_chrM|Schizosaccharomyces_pombe_MTRSchizosaccharomyces_pombe_AB325691' | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o L1981-210117L07_GM18_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.bam | egrep -v 'sacCer3_chrM|Candida_glabrata_mito|Schizosaccharomyces_pombe_chrM|Schizosaccharomyces_pombe_MTRSchizosaccharomyces_pombe_AB325691' | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o L1982-210117L08_GM19_SC-RAF-GAL_AB03.1x36mers.sacCer3.unique.nochrM.bam