python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-MPP8_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-MPP8_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-MPP8_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-MPP8_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-NTC_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-NTC_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-NTC_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-NTC_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_12.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_12.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_sg2_12.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_sg2_12.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_sg2_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_sg2_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_sgALL_12.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_sgALL_12.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Parental_sgALL_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Parental_sgALL_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Phln_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Phln_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-Phln_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-Phln_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-SETDB1_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-SETDB1_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-SETDB1_4.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-SETDB1_4.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-TASOR_4.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-TASOR_4.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 RNA-seq-TASOR_5.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.RNA-seq-TASOR_5.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS88_RNA-seq-hiPSC_WTC-11_non-targeting_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS88_RNA-seq-hiPSC_WTC-11_non-targeting_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS89_RNA-seq-hiPSC_WTC-11_non-targeting_sgRNA_sg18.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS89_RNA-seq-hiPSC_WTC-11_non-targeting_sgRNA_sg18.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS90_RNA-seq-hiPSC_WTC-11_TASOR_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS90_RNA-seq-hiPSC_WTC-11_TASOR_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS91_RNA-seq-hiPSC_WTC-11_TASOR_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS91_RNA-seq-hiPSC_WTC-11_TASOR_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS92_RNA-seq-hiPSC_WTC-11_TASOR2_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS92_RNA-seq-hiPSC_WTC-11_TASOR2_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS93_RNA-seq-hiPSC_WTC-11_TASOR2_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS93_RNA-seq-hiPSC_WTC-11_TASOR2_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS94_RNA-seq-hiPSC_WTC-11_MPP8_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS94_RNA-seq-hiPSC_WTC-11_MPP8_sgRNA_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS95_RNA-seq-hiPSC_WTC-11_MPP8_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS95_RNA-seq-hiPSC_WTC-11_MPP8_sgRNA_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM