/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4412-HFF_MOI3_96hpi_noPFA_3.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4413-HFF_MOI3_96hpi_noPFA_4.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4414-HFF_MOI3_120hpi_noPFA_3.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4415-HFF_MOI3_120hpi_noPFA_4.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4416-HFF_MOI3_72hpi_1hPFA_3.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4417-HFF_MOI3_72hpi_1hPFA_4.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4418-HFF_MOI3_72hpi_48hPFA_3.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4419-HFF_MOI3_72hpi_48hPFA_4.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4420-HFF_MOI0.2_120hpi_noPFA_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4421-HFF_MOI0.2_120hpi_noPFA_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4422-MRC5_0.2_120hpi_noPFA_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4423-MRC5_0.2_120hpi_noPFA_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4424-HFF_MOI3_4hpi_siRNA_ctrl_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4425-HFF_MOI3_4hpi_siRNA_ctrl_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4426-HFF_MOI3_72hpi_siRNA_ctrl_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4427-HFF_MOI3_72hpi_siRNA_ctrl_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4428-HFF_MOI3_4hpi_siRNA_NRF1_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4429-HFF_MOI3_4hpi_siRNA_NRF1_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4430-HFF_MOI3_72hpi_siRNA_NRF1_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4431-HFF_MOI3_72hpi_siRNA_NRF1_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4432-HFF_MOI3_4hpi_siRNA_CTCF_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4433-HFF_MOI3_4hpi_siRNA_CTCF_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4434-HFF_MOI3_72hpi_siRNA_CTCF_1.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4435-HFF_MOI3_72hpi_siRNA_CTCF_2.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4436-K562_130K_NLSx3_L1_CseDa01_L1_NLSx3_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4437-K562_130K_NLSx3_L1_N1CseDa01_L2_FRB_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4438-K562_130K_L1_FKBP12_C1CseDa01_L1_NLSx3_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4439-K562_130K_NLSx3_L1_N2CseDa01_L2_FRB_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4440-K562_130K_L1_FKBP12_C2CseDa01_L1_NLSx3_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4441-K562_130K_NLSx3_L1_N3CseDa01_L2_FRB_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4442-K562_130K_L1_FKBP12_C3CseDa01_L1_NLSx3_5uL.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4443-K562_130K_NLSx3_L1_N1CseDa01_L2_FRB_L1_FKBP12_C1CseDa01_L1_NLSx3_RAPA.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4444-K562_130K_NLSx3_L1_N2CseDa01_L2_FRB_L1_FKBP12_C2CseDa01_L1_NLSx3_RAPA.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38.fa L4445-K562_130K_NLSx3_L1_N3CseDa01_L2_FRB_L1_FKBP12_C3CseDa01_L1_NLSx3_RAPA.2x75mers-trimmed.bwameth.hg38.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4412-HFF_MOI3_96hpi_noPFA_3.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4413-HFF_MOI3_96hpi_noPFA_4.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4414-HFF_MOI3_120hpi_noPFA_3.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4415-HFF_MOI3_120hpi_noPFA_4.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4416-HFF_MOI3_72hpi_1hPFA_3.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4417-HFF_MOI3_72hpi_1hPFA_4.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4418-HFF_MOI3_72hpi_48hPFA_3.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4419-HFF_MOI3_72hpi_48hPFA_4.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4420-HFF_MOI0.2_120hpi_noPFA_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4421-HFF_MOI0.2_120hpi_noPFA_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4422-MRC5_0.2_120hpi_noPFA_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4423-MRC5_0.2_120hpi_noPFA_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4424-HFF_MOI3_4hpi_siRNA_ctrl_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4425-HFF_MOI3_4hpi_siRNA_ctrl_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4426-HFF_MOI3_72hpi_siRNA_ctrl_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4427-HFF_MOI3_72hpi_siRNA_ctrl_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4428-HFF_MOI3_4hpi_siRNA_NRF1_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4429-HFF_MOI3_4hpi_siRNA_NRF1_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4430-HFF_MOI3_72hpi_siRNA_NRF1_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4431-HFF_MOI3_72hpi_siRNA_NRF1_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4432-HFF_MOI3_4hpi_siRNA_CTCF_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4433-HFF_MOI3_4hpi_siRNA_CTCF_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4434-HFF_MOI3_72hpi_siRNA_CTCF_1.2x75mers-trimmed.bwameth.HCMV-merlin.bam
/oak/stanford/groups/akundaje/marinovg/programs/MethylDackel/MethylDackel extract --CHH --CHG /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/HCMV/sequence/merlin.fa L4435-HFF_MOI3_72hpi_siRNA_CTCF_2.2x75mers-trimmed.bwameth.HCMV-merlin.bam