export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix OSC_tandem_R1_1-GSM2050823.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 OSC_tandem_R1_1-GSM2050823_1_val_1.fq.gz -2 OSC_tandem_R1_1-GSM2050823_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix OSC_tandem_R1_2-GSM2050824.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 OSC_tandem_R1_2-GSM2050824_1_val_1.fq.gz -2 OSC_tandem_R1_2-GSM2050824_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix OSC_tandem_R2_1-GSM2050825.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 OSC_tandem_R2_1-GSM2050825_1_val_1.fq.gz -2 OSC_tandem_R2_1-GSM2050825_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix OSC_tandem_R2_2-GSM2050826.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 OSC_tandem_R2_2-GSM2050826_1_val_1.fq.gz -2 OSC_tandem_R2_2-GSM2050826_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_McviPI_R1-GSM2050817.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_McviPI_R1-GSM2050817_1_val_1.fq.gz -2 S2_McviPI_R1-GSM2050817_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_SssI_R1-GSM2050818.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_SssI_R1-GSM2050818_1_val_1.fq.gz -2 S2_SssI_R1-GSM2050818_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_tandem_R1_1-GSM2050819.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_tandem_R1_1-GSM2050819_1_val_1.fq.gz -2 S2_tandem_R1_1-GSM2050819_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_tandem_R1_2-GSM2050820.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_tandem_R1_2-GSM2050820_1_val_1.fq.gz -2 S2_tandem_R1_2-GSM2050820_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_tandem_R2_1-GSM2050821.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_tandem_R2_1-GSM2050821_1_val_1.fq.gz -2 S2_tandem_R2_1-GSM2050821_2_val_2.fq.gz
export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch; /oak/stanford/groups/akundaje/marinovg/programs/Bismark-0.18.2/bismark --parallel 3 --bowtie1 -n 1 --gzip --nucleotide_coverage -X 1000 --samtools_path /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --prefix S2_tandem_R2_2-GSM2050822.Bismark-0.18.2 /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bismarck -1 S2_tandem_R2_2-GSM2050822_1_val_1.fq.gz -2 S2_tandem_R2_2-GSM2050822_2_val_2.fq.gz