export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L289-30fL_B_dSMF.sacCer3+C_glabrata_CBS138_current_chromosomes.Bismark_v0.19.0.bt2.clip.pbat ~/Stanford_bootcamp/combined_indexes/bismarck_indexes-bt2 -1 L289-30fL_B_dSMF.end1.75mers_val_1.fq.gz -2 L289-30fL_B_dSMF.end2.75mers_val_2.fq.gz &
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L290-30fL_A_dSMF.sacCer3+C_glabrata_CBS138_current_chromosomes.Bismark_v0.19.0.bt2.clip.pbat ~/Stanford_bootcamp/combined_indexes/bismarck_indexes-bt2 -1 L290-30fL_A_dSMF.end1.75mers_val_1.fq.gz -2 L290-30fL_A_dSMF.end2.75mers_val_2.fq.gz &
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L291-60fL_D_dSMF.sacCer3+C_glabrata_CBS138_current_chromosomes.Bismark_v0.19.0.bt2.clip.pbat ~/Stanford_bootcamp/combined_indexes/bismarck_indexes-bt2 -1 L291-60fL_D_dSMF.end1.75mers_val_1.fq.gz -2 L291-60fL_D_dSMF.end2.75mers_val_2.fq.gz &
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L292-90fL_E_dSMF.sacCer3+C_glabrata_CBS138_current_chromosomes.Bismark_v0.19.0.bt2.clip.pbat ~/Stanford_bootcamp/combined_indexes/bismarck_indexes-bt2 -1 L292-90fL_E_dSMF.end1.75mers_val_1.fq.gz -2 L292-90fL_E_dSMF.end2.75mers_val_2.fq.gz &
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L293-90fL_F_dSMF.sacCer3+C_glabrata_CBS138_current_chromosomes.Bismark_v0.19.0.bt2.clip.pbat ~/Stanford_bootcamp/combined_indexes/bismarck_indexes-bt2 -1 L293-90fL_F_dSMF.end1.75mers_val_1.fq.gz -2 L293-90fL_F_dSMF.end2.75mers_val_2.fq.gz &