export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 3 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix L180-dSMF.Saccharomyces_paradoxus-SGD.Bismark_v0.19.0.bowtie2.clip.pbat /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Saccharomyces_paradoxus-SGD/bismarck_indexes-BT2 -1 L180_S1_L001_R1_001_val_1.fq.gz -2 L180_S1_L001_R2_001_val_2.fq.gz
export PATH=$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 L198-dSMF.sacCer3.Bismark_v0.19.0.bowtie2.clip.pbat /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bismarck_indexes-BT2 -1 Undetermined_S0_L001_R1_001_val_1.fq.gz -2 Undetermined_S0_L001_R2_001_val_2.fq.gz