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/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 Stage_5_validation-GSM848929-Bismark_v0.19.0.bowtie2.droprep.untrimmed_bt2.bam