export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_kawagutii_25C-GSM2801017.Bismark_v0.19.0.bowtie2.pbat /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bismark-indexes-BT2 --single_end  SRR6123441_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_kawagutii_32C-GSM2801018.Bismark_v0.19.0.bowtie2.pbat /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bismark-indexes-BT2 --single_end  SRR6123442_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_minutum_25C-GSM2801019.Bismark_v0.19.0.bowtie2.pbat /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_kawagutii_assembly/bismark-indexes-BT2 --single_end  SRR6123443_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --pbat --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_minutum_30C-GSM2801020.Bismark_v0.19.0.bowtie2.pbat /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_kawagutii_assembly/bismark-indexes-BT2 --single_end  SRR6123444_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_kawagutii_25C-GSM2801017.Bismark_v0.19.0.bowtie2 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bismark-indexes-BT2 --single_end SRR6123441_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_kawagutii_32C-GSM2801018.Bismark_v0.19.0.bowtie2 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bismark-indexes-BT2 --single_end SRR6123442_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_minutum_25C-GSM2801019.Bismark_v0.19.0.bowtie2 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_kawagutii_assembly/bismark-indexes-BT2 --single_end SRR6123443_1_trimmed.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.2.0; /oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark --parallel 8 --bowtie2 --nucleotide_coverage --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools --prefix mC_S_minutum_30C-GSM2801020.Bismark_v0.19.0.bowtie2 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_kawagutii_assembly/bismark-indexes-BT2 --single_end SRR6123444_1_trimmed.fq.gz