/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck dnmt2-PGT45-GSM983095-Bismark_v0.19.0.bowtie1.clip.drorep.pbat.SRR535803_1_val_1_bismark_pe.bam
/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck dnmt2-PGT45-GSM983095-Bismark_v0.19.0.bowtie1.clip.drorep.SRR535803_1_val_1_bismark_pe.bam
/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck-BT2 dnmt2-PGT45-GSM983095-Bismark_v0.19.0.bowtie2.clip.drorep.pbat.SRR535803_1_val_1_bismark_bt2_pe.bam
/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck w1118-PGT44-GSM983094-Bismark_v0.19.0.bowtie1.clip.drorep.pbat.SRR535802_1_val_1_bismark_pe.bam
/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck w1118-PGT44-GSM983094-Bismark_v0.19.0.bowtie1.clip.drorep.SRR535802_1_val_1_bismark_pe.bam
/oak/stanford/groups/akundaje/marinovg/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /oak/stanford/groups/akundaje/marinovg/genomes/repeats/RepBase17.08.fasta/drorep-Bismarck-BT2 w1118-PGT44-GSM983094-Bismark_v0.19.0.bowtie2.clip.drorep.pbat.SRR535802_1_val_1_bismark_bt2_pe.bam