python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2017-Red_necked_wallaby-Sample2873-Rep1.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2017-Red_necked_wallaby-Sample2873-Rep1.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macropus_rufogriseus-Macropus_rufogriseus_HiC/Macropus_rufogriseus-Macropus_rufogriseus_HiC.chrom.sizes L2017-Red_necked_wallaby-Sample2873-Rep1.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2018-Red_necked_wallaby-Sample2873-Rep2.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2018-Red_necked_wallaby-Sample2873-Rep2.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macropus_rufogriseus-Macropus_rufogriseus_HiC/Macropus_rufogriseus-Macropus_rufogriseus_HiC.chrom.sizes L2018-Red_necked_wallaby-Sample2873-Rep2.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L878-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L878-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macropus_rufogriseus-Macropus_rufogriseus_HiC/Macropus_rufogriseus-Macropus_rufogriseus_HiC.chrom.sizes L878-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L879-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L879-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macropus_rufogriseus-Macropus_rufogriseus_HiC/Macropus_rufogriseus-Macropus_rufogriseus_HiC.chrom.sizes L879-Bennetts_wallaby_ID_TCH4030_Sample2413_Macropus_rufogriseus.2x36mers.Macropus_rufogriseus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L872-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L872-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Peromyscus_eremicus-Peer1.6.0_HiC/Peromyscus_eremicus-Peer1.6.0_HiC.chrom.sizes L872-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L873-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L873-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Peromyscus_eremicus-Peer1.6.0_HiC/Peromyscus_eremicus-Peer1.6.0_HiC.chrom.sizes L873-Cactus_mouse_Sample2404_Peromyscus_eremicus.2x36mers.Peer1.6.0_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L882-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L882-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Osgoodomys_banderanus-Osgoodomys_banderanus_1k/Osgoodomys_banderanus-Osgoodomys_banderanus_1k.chrom.sizes L882-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L883-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L883-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Osgoodomys_banderanus-Osgoodomys_banderanus_1k/Osgoodomys_banderanus-Osgoodomys_banderanus_1k.chrom.sizes L883-Michoacan_Deer_Mouse_ID_TCH3380_Sample2401_Osgoodomys_banderanus.2x36mers.Osgoodomys_banderanus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L888-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L888-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mus_shortridgei-Mus_shortridgei_1k/Mus_shortridgei-Mus_shortridgei_1k.chrom.sizes L888-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L889-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L889-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mus_shortridgei-Mus_shortridgei_1k/Mus_shortridgei-Mus_shortridgei_1k.chrom.sizes L889-Shortridges_mouse_ID_2223_Sample2416_Mus_shortridgei.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L902-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L902-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_yumanensis-Myotis_yumanensis_HiC/Myotis_yumanensis-Myotis_yumanensis_HiC.chrom.sizes L902-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L903-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L903-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_yumanensis-Myotis_yumanensis_HiC/Myotis_yumanensis-Myotis_yumanensis_HiC.chrom.sizes L903-Myotis_yumanensis_Yuma_myotisID_MYUMP4_Sample2431.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2005-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep1.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2005-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep1.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Ammospermophilus_harrisii-Ammospermophilus_harrisii_1k/Ammospermophilus_harrisii-Ammospermophilus_harrisii_1k.chrom.sizes L2005-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep1.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2006-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep2.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2006-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep2.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Ammospermophilus_harrisii-Ammospermophilus_harrisii_1k/Ammospermophilus_harrisii-Ammospermophilus_harrisii_1k.chrom.sizes L2006-Harris_antelope_squirrel_Ammospermophilus_harrisii-Sample2869-Rep2.2x36mers.Ammospermophilus_harrisii_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2009-Field_Vole-Sample2585-Rep1.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2009-Field_Vole-Sample2585-Rep1.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC.chrom.sizes L2009-Field_Vole-Sample2585-Rep1.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2010-Field_Vole-Sample2585-Rep2.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2010-Field_Vole-Sample2585-Rep2.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC.chrom.sizes L2010-Field_Vole-Sample2585-Rep2.2x36mers.GCA_001305995.1_ASM130599v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2013-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep1.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2013-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep1.2x36mers.Myotis_yumanensis_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_yumanensis-Myotis_yumanensis_HiC/Myotis_yumanensis-Myotis_yumanensis_HiC.chrom.sizes L2013-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep1.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2014-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep2.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2014-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep2.2x36mers.Myotis_yumanensis_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_yumanensis-Myotis_yumanensis_HiC/Myotis_yumanensis-Myotis_yumanensis_HiC.chrom.sizes L2014-Myotis_yumanensis_S2431_P1_7-9-19_RK-Sample2431-Rep2.2x36mers.Myotis_yumanensis_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2015-Montane_Vole-Sample2587-Rep1.2x36mers.Microtus_montanus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2015-Montane_Vole-Sample2587-Rep1.2x36mers.Microtus_montanus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Microtus_montanus-Microtus_montanus_1k/Microtus_montanus-Microtus_montanus_1k.chrom.sizes L2015-Montane_Vole-Sample2587-Rep1.2x36mers.Microtus_montanus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2016-Montane_Vole-Sample2587-Rep2.2x36mers.Microtus_montanus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2016-Montane_Vole-Sample2587-Rep2.2x36mers.Microtus_montanus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Microtus_montanus-Microtus_montanus_1k/Microtus_montanus-Microtus_montanus_1k.chrom.sizes L2016-Montane_Vole-Sample2587-Rep2.2x36mers.Microtus_montanus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2019-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep1.2x36mers.Myotis_evotis_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2019-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep1.2x36mers.Myotis_evotis_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_evotis-Myotis_evotis_1k/Myotis_evotis-Myotis_evotis_1k.chrom.sizes L2019-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep1.2x36mers.Myotis_evotis_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2020-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep2.2x36mers.Myotis_evotis_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2020-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep2.2x36mers.Myotis_evotis_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myotis_evotis-Myotis_evotis_1k/Myotis_evotis-Myotis_evotis_1k.chrom.sizes L2020-Myotis_evotis_S2429_P2_7-15-19_0.5M_AO-Sample2429-Rep2.2x36mers.Myotis_evotis_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2025-Stoat_Mustela_erminea-Sample2591-Rep1.2x36mers.Mustela_erminea_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2025-Stoat_Mustela_erminea-Sample2591-Rep1.2x36mers.Mustela_erminea_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mustela_erminea-Mustela_erminea_HiC/Mustela_erminea-Mustela_erminea_HiC.chrom.sizes L2025-Stoat_Mustela_erminea-Sample2591-Rep1.2x36mers.Mustela_erminea_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2026-Stoat_Mustela_erminea-Sample2591-Rep2.2x36mers.Mustela_erminea_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2026-Stoat_Mustela_erminea-Sample2591-Rep2.2x36mers.Mustela_erminea_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mustela_erminea-Mustela_erminea_HiC/Mustela_erminea-Mustela_erminea_HiC.chrom.sizes L2026-Stoat_Mustela_erminea-Sample2591-Rep2.2x36mers.Mustela_erminea_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2031-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep1.2x36mers.Myodes_rutilus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2031-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep1.2x36mers.Myodes_rutilus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myodes_rutilus-Myodes_rutilus_HiC/Myodes_rutilus-Myodes_rutilus_HiC.chrom.sizes L2031-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep1.2x36mers.Myodes_rutilus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2032-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep2.2x36mers.Myodes_rutilus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2032-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep2.2x36mers.Myodes_rutilus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Myodes_rutilus-Myodes_rutilus_HiC/Myodes_rutilus-Myodes_rutilus_HiC.chrom.sizes L2032-Northern_red-backed_vole_Myodes_previously_Clethrionomys_rutilus-Sample2596-Rep2.2x36mers.Myodes_rutilus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2039-Jamaican_fruit_bat-Sample2892-Rep1.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2039-Jamaican_fruit_bat-Sample2892-Rep1.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.chrom.sizes L2039-Jamaican_fruit_bat-Sample2892-Rep1.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2040-Jamaican_fruit_bat-Sample2892-Rep2.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2040-Jamaican_fruit_bat-Sample2892-Rep2.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.chrom.sizes L2040-Jamaican_fruit_bat-Sample2892-Rep2.2x36mers.GCA_014825515.1_WHU_Ajam_v2_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2043-Desert_bighorned_sheep-Sample2891-Rep1.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2043-Desert_bighorned_sheep-Sample2891-Rep1.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.chrom.sizes L2043-Desert_bighorned_sheep-Sample2891-Rep1.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2044-Desert_bighorned_sheep-Sample2891-Rep2.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2044-Desert_bighorned_sheep-Sample2891-Rep2.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.chrom.sizes L2044-Desert_bighorned_sheep-Sample2891-Rep2.2x36mers.GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2045-Midday_Gerbil-Sample2582-Rep1.2x36mers.Meriones_meridianus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2045-Midday_Gerbil-Sample2582-Rep1.2x36mers.Meriones_meridianus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Meriones_meridianus-Meriones_meridianus_1k/Meriones_meridianus-Meriones_meridianus_1k.chrom.sizes L2045-Midday_Gerbil-Sample2582-Rep1.2x36mers.Meriones_meridianus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2046-Midday_Gerbil-Sample2582-Rep2.2x36mers.Meriones_meridianus_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2046-Midday_Gerbil-Sample2582-Rep2.2x36mers.Meriones_meridianus_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Meriones_meridianus-Meriones_meridianus_1k/Meriones_meridianus-Meriones_meridianus_1k.chrom.sizes L2046-Midday_Gerbil-Sample2582-Rep2.2x36mers.Meriones_meridianus_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2051-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep1.2x36mers.Eulemur_macaco_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2051-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep1.2x36mers.Eulemur_macaco_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Eulemur_macaco-Eulemur_macaco_HiC/Eulemur_macaco-Eulemur_macaco_HiC.chrom.sizes L2051-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep1.2x36mers.Eulemur_macaco_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2052-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep2.2x36mers.Eulemur_macaco_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2052-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep2.2x36mers.Eulemur_macaco_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Eulemur_macaco-Eulemur_macaco_HiC/Eulemur_macaco-Eulemur_macaco_HiC.chrom.sizes L2052-Black_lemur_Eulemur_macaco_rufus-Sample2600-Rep2.2x36mers.Eulemur_macaco_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2053-Sonoran_Woodrat-Sample2584-Rep1.2x36mers.Neotoma_phenax_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2053-Sonoran_Woodrat-Sample2584-Rep1.2x36mers.Neotoma_phenax_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Neotoma_phenax-Neotoma_phenax_HiC/Neotoma_phenax-Neotoma_phenax_HiC.chrom.sizes L2053-Sonoran_Woodrat-Sample2584-Rep1.2x36mers.Neotoma_phenax_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2054-Sonoran_Woodrat-Sample2584-Rep2.2x36mers.Neotoma_phenax_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2054-Sonoran_Woodrat-Sample2584-Rep2.2x36mers.Neotoma_phenax_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Neotoma_phenax-Neotoma_phenax_HiC/Neotoma_phenax-Neotoma_phenax_HiC.chrom.sizes L2054-Sonoran_Woodrat-Sample2584-Rep2.2x36mers.Neotoma_phenax_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2147-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2147-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mus_shortridgei-Mus_shortridgei_1k/Mus_shortridgei-Mus_shortridgei_1k.chrom.sizes L2147-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2159-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2159-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Mus_shortridgei-Mus_shortridgei_1k/Mus_shortridgei-Mus_shortridgei_1k.chrom.sizes L2159-Mus_shortridgei-Shortridge_mouse-Sample2416.2x36mers.Mus_shortridgei_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2174-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2174-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/Cercopithecus_campbelli-Cercopithecus_campbelli_HiC.chrom.sizes L2174-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2186-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2186-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/Cercopithecus_campbelli-Cercopithecus_campbelli_HiC.chrom.sizes L2186-Cercopithecus_campbelli-Campbell_monkey-Sample3917.2x36mers.Cercopithecus_campbelli_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2177-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2177-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC.chrom.sizes L2177-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2189-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2189-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC.chrom.sizes L2189-Meriones_unguiculatus-Mongolian_gerbil-Sample3928.2x36mers.GCA_008131255.1_ASM813125v1_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2196-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2196-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Euderma_maculatum-Euderma_maculatum_1k/Euderma_maculatum-Euderma_maculatum_1k.chrom.sizes L2196-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2208-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2208-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Euderma_maculatum-Euderma_maculatum_1k/Euderma_maculatum-Euderma_maculatum_1k.chrom.sizes L2208-Euderma_maculatum-Spotted_bat-Sample2871.2x36mers.Euderma_maculatum_1k.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2200-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2200-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Lasiurus_seminolus-Lasiurus_seminolus_HiC/Lasiurus_seminolus-Lasiurus_seminolus_HiC.chrom.sizes L2200-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2212-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2212-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Lasiurus_seminolus-Lasiurus_seminolus_HiC/Lasiurus_seminolus-Lasiurus_seminolus_HiC.chrom.sizes L2212-Lasiurus_xxx-Hairy-tailed_bat-Sample4314.2x36mers.Lasiurus_seminolus_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2219-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2219-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.chrom.sizes L2219-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py L2231-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.narrowPeak 0 L2231-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.chrom.sizes L2231-Sigmodon_hispidus-Hispid_cotton_rat-Sample4102.2x36mers.GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC.unique.dedup.MACS-2.1.0_peaks.RPM -RPM -uniqueBAM &