/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1910-GM16_Haematodinium_DVNP_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1910-GM16_Haematodinium_DVNP_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1911-GM16_Haematodinium_DVNP_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1911-GM16_Haematodinium_DVNP_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1912-GM16_Haematodinium_DVNP_ON_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1912-GM16_Haematodinium_DVNP_ON_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1913-GM16_Haematodinium_DVNP_ON_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1913-GM16_Haematodinium_DVNP_ON_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1914-GM17_vehcile_DVNP_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1914-GM17_vehcile_DVNP_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1915-GM17_vehcile_DVNP_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1915-GM17_vehcile_DVNP_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1916-GM17_vehcile_DVNP_ON_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1916-GM17_vehcile_DVNP_ON_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1917-GM17_vehcile_DVNP_ON_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1917-GM17_vehcile_DVNP_ON_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1918-GM18_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1918-GM18_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1919-GM18_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1919-GM18_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1920-GM19_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1920-GM19_rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view L1921-GM19_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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/Stanford_bootcamp/combined_indexes/sacCer3+C_glabrata_CBS138_current_chromosomes.fa - -o L1921-GM19_rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.nochrM.bam