python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep1-GSM2706045.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep1-GSM2706045.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep1-GSM2706045.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep2-GSM2706046.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep2-GSM2706046.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2-AbdA_HA-AbdA_ChIPSeq_Rep2-GSM2706046.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep1-GSM2706059.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep1-GSM2706059.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep1-GSM2706059.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep2-GSM2706060.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep2-GSM2706060.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2_GAGA_ChIPSeq_Rep2-GSM2706060.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep1-GSM2706055.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep1-GSM2706055.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep1-GSM2706055.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep2-GSM2706056.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep2-GSM2706056.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2_M1BP_ChIPSeq_Rep2-GSM2706056.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep1-GSM2706083.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep1-GSM2706083.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep1-GSM2706083.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep2-GSM2706084.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep2-GSM2706084.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 01-S2-AbdA-GSE101557/S2-Ubx_HA-Ubx_ChIPSeq_Rep2-GSM2706084.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 02-modENCODE-CTCF-GSE20000/S2_CTCF200_ChIPSeq_1_and_2-GSM499649.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 02-modENCODE-CTCF-GSE20000/S2_CTCF200_ChIPSeq_1_and_2-GSM499649.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 02-modENCODE-CTCF-GSE20000/S2_CTCF200_ChIPSeq_1_and_2-GSM499649.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 02-modENCODE-CTCF-GSE20000/S2_CTCF500_ChIPSeq_1_and_2-GSM499651.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 02-modENCODE-CTCF-GSE20000/S2_CTCF500_ChIPSeq_1_and_2-GSM499651.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 02-modENCODE-CTCF-GSE20000/S2_CTCF500_ChIPSeq_1_and_2-GSM499651.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_1_extraction1_seq1_aliquote_1-GSM522353.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_1_extraction1_seq1_aliquote_1-GSM522353.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_1_extraction1_seq1_aliquote_1-GSM522353.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_2_extraction2_seq1_aliquote_1-GSM522354.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_2_extraction2_seq1_aliquote_1-GSM522354.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 03-modENCODE-ORC2-GSE20887/ORC2_S2_DRSC_2_extraction2_seq1_aliquote_1-GSM522354.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 06-HSF-GSE19025/S2_20HS_HSF_IP-GSM470839.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 06-HSF-GSE19025/S2_20HS_HSF_IP-GSM470839.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 06-HSF-GSE19025/S2_20HS_HSF_IP-GSM470839.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 06-HSF-GSE19025/S2_NHS_HSF_IP-GSM470841.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 06-HSF-GSE19025/S2_NHS_HSF_IP-GSM470841.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 06-HSF-GSE19025/S2_NHS_HSF_IP-GSM470841.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 06-HSF-GSE19025/S2_NHS_HSF_KD-IP-GSM470842.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 06-HSF-GSE19025/S2_NHS_HSF_KD-IP-GSM470842.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 06-HSF-GSE19025/S2_NHS_HSF_KD-IP-GSM470842.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 07-SuHw-GSE27679/SuHw-p1a..p1b-GSM685611.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 07-SuHw-GSE27679/SuHw-p1a..p1b-GSM685611.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 07-SuHw-GSE27679/SuHw-p1a..p1b-GSM685611.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 07-SuHw-GSE27679/SuHw-s1..s7-GSM685610.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 07-SuHw-GSE27679/SuHw-s1..s7-GSM685610.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 07-SuHw-GSE27679/SuHw-s1..s7-GSM685610.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_dUTX663_3-GSM1017401.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_dUTX663_3-GSM1017401.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_dUTX663_3-GSM1017401.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K27ac_1-GSM1017404.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K27ac_1-GSM1017404.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K27ac_1-GSM1017404.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K27ac_2-GSM1017405.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K27ac_2-GSM1017405.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K27ac_2-GSM1017405.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K27me3_4-GSM1017406.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K27me3_4-GSM1017406.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K27me3_4-GSM1017406.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K4me1_1-GSM1017407.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K4me1_1-GSM1017407.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K4me1_1-GSM1017407.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K4me1_4-GSM1017408.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K4me1_4-GSM1017408.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K4me1_4-GSM1017408.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K4me3_5-GSM1017409.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K4me3_5-GSM1017409.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K4me3_5-GSM1017409.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_H3K4me3_6-GSM1017410.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_H3K4me3_6-GSM1017410.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_H3K4me3_6-GSM1017410.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_LPT470_3-GSM1017402.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_LPT470_3-GSM1017402.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_LPT470_3-GSM1017402.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_RNAPolII_5-GSM1017403.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_RNAPolII_5-GSM1017403.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_RNAPolII_5-GSM1017403.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 08-Trr-GSE41440/WT_Trr_6-GSM1017400.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 08-Trr-GSE41440/WT_Trr_6-GSM1017400.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 08-Trr-GSE41440/WT_Trr_6-GSM1017400.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 09-PSC-PH-GSE38166/PH_control_S2-PH_ChIPSeq-GSM936123.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 09-PSC-PH-GSE38166/PH_control_S2-PH_ChIPSeq-GSM936123.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 09-PSC-PH-GSE38166/PH_control_S2-PH_ChIPSeq-GSM936123.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_1-GSM936116.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_1-GSM936116.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_1-GSM936116.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_2-GSM936117.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_2-GSM936117.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 09-PSC-PH-GSE38166/PSC_control_S2_ChIPSeq_replicate_2-GSM936117.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 09-PSC-PH-GSE38166/PSC_mitotic_S2_ChIPSeq_replicate_1-GSM936114.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 09-PSC-PH-GSE38166/PSC_mitotic_S2_ChIPSeq_replicate_1-GSM936114.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 09-PSC-PH-GSE38166/PSC_mitotic_S2_ChIPSeq_replicate_1-GSM936114.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1C-GSM764316.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1C-GSM764316.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1C-GSM764316.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1N-GSM764317.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1N-GSM764317.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 10-Ash1-GSE30820/DmS2DRSC_ChIP_Ash1N-GSM764317.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID166-GSM764318.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID166-GSM764318.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID166-GSM764318.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID173-GSM764319.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID173-GSM764319.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 10-Ash1-GSE30820/DmS2DRSC_ChIP_FSH_ID173-GSM764319.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 11-GAF-GSE40646/GAF_ChIP-seq-GSM998826.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 11-GAF-GSE40646/GAF_ChIP-seq-GSM998826.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 11-GAF-GSE40646/GAF_ChIP-seq-GSM998826.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 11-GAF-GSE40646/GAF-KD_GAF_ChIP-seq-GSM998827.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 11-GAF-GSE40646/GAF-KD_GAF_ChIP-seq-GSM998827.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 11-GAF-GSE40646/GAF-KD_GAF_ChIP-seq-GSM998827.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217677.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217677.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217677.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217678.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217678.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 12-modENCODE-H3K4me3-GSE50369/H3K4me3_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217678.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 13-CP190-GSE52886/CP190-mut-GSM1277520.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 13-CP190-GSE52886/CP190-mut-GSM1277520.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 13-CP190-GSE52886/CP190-mut-GSM1277520.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 13-CP190-GSE52886/CP190-WT1-GSM1277517.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 13-CP190-GSE52886/CP190-WT1-GSM1277517.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 13-CP190-GSE52886/CP190-WT1-GSM1277517.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 13-CP190-GSE52886/CP190-WT2-GSM1277518.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 13-CP190-GSE52886/CP190-WT2-GSM1277518.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 13-CP190-GSE52886/CP190-WT2-GSM1277518.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 14-CP190-GSE46614/CG8436-GSM1133264.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 14-CP190-GSE46614/CG8436-GSM1133264.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 14-CP190-GSE46614/CG8436-GSM1133264.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 14-CP190-GSE46614/CG9740-GSM1133265.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 14-CP190-GSE46614/CG9740-GSM1133265.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 14-CP190-GSE46614/CG9740-GSM1133265.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 14-CP190-GSE46614/CP190-GSM1133263.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 14-CP190-GSE46614/CP190-GSM1133263.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 14-CP190-GSE46614/CP190-GSM1133263.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 15-Yki-GSE46305/Yki_S2_ChIP_rep2-GSM1128468.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 15-Yki-GSE46305/Yki_S2_ChIP_rep2-GSM1128468.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 15-Yki-GSE46305/Yki_S2_ChIP_rep2-GSM1128468.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 16-Pita-Zpici-GSE54337/ChIP-seq_of_Pita_in_S2_cells-GSM1313420.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 16-Pita-Zpici-GSE54337/ChIP-seq_of_Pita_in_S2_cells-GSM1313420.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 16-Pita-Zpici-GSE54337/ChIP-seq_of_Pita_in_S2_cells-GSM1313420.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 16-Pita-Zpici-GSE54337/ChIP-seq_of_ZIPIC_in_S2_cells-GSM1313421.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 16-Pita-Zpici-GSE54337/ChIP-seq_of_ZIPIC_in_S2_cells-GSM1313421.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 16-Pita-Zpici-GSE54337/ChIP-seq_of_ZIPIC_in_S2_cells-GSM1313421.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_1-GSM1333889.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_1-GSM1333889.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_1-GSM1333889.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_2-GSM1430012.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_2-GSM1430012.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 17-ChIP-nexus-GSE55306/Max_ChIP-nexus_Rep_2-GSM1430012.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 17-ChIP-nexus-GSE55306/Max_ChIP-seq_Rep_1-GSM1341815.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 17-ChIP-nexus-GSE55306/Max_ChIP-seq_Rep_1-GSM1341815.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 17-ChIP-nexus-GSE55306/Max_ChIP-seq_Rep_1-GSM1341815.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_1-GSM1333890.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_1-GSM1333890.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_1-GSM1333890.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_2-GSM1430013.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_2-GSM1430013.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 17-ChIP-nexus-GSE55306/Myc_ChIP-nexus_Rep_2-GSM1430013.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 18-Z4-GSE49102/Dsk2-GSM1193815.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 18-Z4-GSE49102/Dsk2-GSM1193815.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 18-Z4-GSE49102/Dsk2-GSM1193815.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 18-Z4-GSE49102/HP1c-GSM1193816.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 18-Z4-GSE49102/HP1c-GSM1193816.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 18-Z4-GSE49102/HP1c-GSM1193816.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 18-Z4-GSE49102/ROW-GSM1193811.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 18-Z4-GSE49102/ROW-GSM1193811.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 18-Z4-GSE49102/ROW-GSM1193811.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 18-Z4-GSE49102/WOC-GSM1193810.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 18-Z4-GSE49102/WOC-GSM1193810.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 18-Z4-GSE49102/WOC-GSM1193810.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 18-Z4-GSE49102/Z4-GSM1193812.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 18-Z4-GSE49102/Z4-GSM1193812.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 18-Z4-GSE49102/Z4-GSM1193812.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate1-GSM1616472.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate1-GSM1616472.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate1-GSM1616472.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate2-GSM1616474.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate2-GSM1616474.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 19-Scm-GSE66183/BioTAP-N-Scm_IP_S2_replicate2-GSM1616474.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 19-Scm-GSE66183/Pc-C-BioTAP_IP_S2_replicate1-GSM1616476.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 19-Scm-GSE66183/Pc-C-BioTAP_IP_S2_replicate1-GSM1616476.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 19-Scm-GSE66183/Pc-C-BioTAP_IP_S2_replicate1-GSM1616476.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 21-CBP-GSE64464/CBP-rb_ChIP-seq-GSM1571852.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 21-CBP-GSE64464/CBP-rb_ChIP-seq-GSM1571852.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 21-CBP-GSE64464/CBP-rb_ChIP-seq-GSM1571852.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485019.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485019.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485019.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485020.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485020.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 22-PH-GSE60686/PH-WT_ChIP-seq-GSM1485020.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 23-dCAP-D3-GSE74413/dCAP-D3_ChIP_1-GSM1919990.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 23-dCAP-D3-GSE74413/dCAP-D3_ChIP_1-GSM1919990.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 23-dCAP-D3-GSE74413/dCAP-D3_ChIP_1-GSM1919990.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 24-Nup98-GSE94922/Nup98_S2-GSM2491983.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 24-Nup98-GSE94922/Nup98_S2-GSM2491983.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 24-Nup98-GSE94922/Nup98_S2-GSM2491983.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 24-Nup98-GSE94922/Nup98_S2_OE-GSM2491984.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 24-Nup98-GSE94922/Nup98_S2_OE-GSM2491984.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 24-Nup98-GSE94922/Nup98_S2_OE-GSM2491984.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 25-MSL2-GSE94115/ChIP_H4K16ac_S2_rep1-GSM2469508.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 25-MSL2-GSE94115/ChIP_H4K16ac_S2_rep1-GSM2469508.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 25-MSL2-GSE94115/ChIP_H4K16ac_S2_rep1-GSM2469508.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 25-MSL2-GSE94115/ChIP_MSL2_S2_rep1-GSM2469507.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 25-MSL2-GSE94115/ChIP_MSL2_S2_rep1-GSM2469507.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 25-MSL2-GSE94115/ChIP_MSL2_S2_rep1-GSM2469507.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 25-MSL2-GSE94115/ChIP_MSL2_S2_rep2-GSM2469510.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 25-MSL2-GSE94115/ChIP_MSL2_S2_rep2-GSM2469510.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 25-MSL2-GSE94115/ChIP_MSL2_S2_rep2-GSM2469510.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 25-MSL2-GSE94115/ChIP_MSL2_S2_rep3-GSM2469512.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 25-MSL2-GSE94115/ChIP_MSL2_S2_rep3-GSM2469512.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 25-MSL2-GSE94115/ChIP_MSL2_S2_rep3-GSM2469512.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 25-MSL2-GSE94115/ChIP_MSL2_S2_rep4-GSM2469514.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 25-MSL2-GSE94115/ChIP_MSL2_S2_rep4-GSM2469514.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 25-MSL2-GSE94115/ChIP_MSL2_S2_rep4-GSM2469514.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 29-Dsx-GSE49480/S2_DsxF-GSM1200247.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 29-Dsx-GSE49480/S2_DsxF-GSM1200247.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 29-Dsx-GSE49480/S2_DsxF-GSM1200247.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 29-Dsx-GSE49480/S2_DsxM-GSM1200248.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 29-Dsx-GSE49480/S2_DsxM-GSM1200248.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 29-Dsx-GSE49480/S2_DsxM-GSM1200248.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep1-GSM1295978.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep1-GSM1295978.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep1-GSM1295978.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep2-GSM1295979.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep2-GSM1295979.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 30-Pc_Pho_GAF_Ad1-GSE47829/Adf1_n-ChIP_S2_rep2-GSM1295979.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 30-Pc_Pho_GAF_Ad1-GSE47829/GAF_n-ChIP_S2_rep2-GSM1295977.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 30-Pc_Pho_GAF_Ad1-GSE47829/GAF_n-ChIP_S2_rep2-GSM1295977.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 30-Pc_Pho_GAF_Ad1-GSE47829/GAF_n-ChIP_S2_rep2-GSM1295977.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 31-BEAF32-GSE52887/Beaf-32-GSM1278639.25mers.unique.MACS-2.1.0_peaks.narrowPeak 0 31-BEAF32-GSE52887/Beaf-32-GSM1278639.25mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 31-BEAF32-GSE52887/Beaf-32-GSM1278639.25mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep1-GSM1296167.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep1-GSM1296167.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep1-GSM1296167.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep2-GSM1296168.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep2-GSM1296168.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 32-dMyc-GSE53560/dMyc_S2-DRSC_late_embryonic_D.melanogaster_ChIP_Rep2-GSM1296168.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 33-insulators-GSE41354/Ct_CP190-GSM1015404.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 33-insulators-GSE41354/Ct_CP190-GSM1015404.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 33-insulators-GSE41354/Ct_CP190-GSM1015404.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 33-insulators-GSE41354/Ct_dCTCF-GSM1015410.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 33-insulators-GSE41354/Ct_dCTCF-GSM1015410.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 33-insulators-GSE41354/Ct_dCTCF-GSM1015410.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 33-insulators-GSE41354/Ct_Mod-GSM1015408.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 33-insulators-GSE41354/Ct_Mod-GSM1015408.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 33-insulators-GSE41354/Ct_Mod-GSM1015408.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 33-insulators-GSE41354/Ct_Su_Hw-GSM1015406.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 33-insulators-GSE41354/Ct_Su_Hw-GSM1015406.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 33-insulators-GSE41354/Ct_Su_Hw-GSM1015406.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217657.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217657.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep1-GSM1217657.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217658.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217658.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 34-CG8478-GSE50364/CG8478_S2_cells_ChIP-seq_ChIP_Rep2-GSM1217658.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1C_ChIP-seq-GSM892448.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1C_ChIP-seq-GSM892448.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1C_ChIP-seq-GSM892448.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1N_ChIP-seq-GSM892447.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1N_ChIP-seq-GSM892447.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 35-ASH1-GSE36404/Dm_S2-DRSC_ASH1N_ChIP-seq-GSM892447.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S_ChIP-seq-GSM892449.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S_ChIP-seq-GSM892449.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S_ChIP-seq-GSM892449.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S+L_ChIP-seq-GSM892450.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S+L_ChIP-seq-GSM892450.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 35-ASH1-GSE36404/Dm_S2-DRSC_FSH-S+L_ChIP-seq-GSM892450.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/mle_1-GSM929155.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/mle_1-GSM929155.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/mle_1-GSM929155.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/mle_2-GSM929156.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/mle_2-GSM929156.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/mle_2-GSM929156.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/mof_1-GSM929153.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/mof_1-GSM929153.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/mof_1-GSM929153.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/mof_2-GSM929154.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/mof_2-GSM929154.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/mof_2-GSM929154.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/msl1_1-GSM929146.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/msl1_1-GSM929146.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/msl1_1-GSM929146.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/msl1_2-GSM929147.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/msl1_2-GSM929147.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/msl1_2-GSM929147.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/msl2_3-GSM929150.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/msl2_3-GSM929150.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/msl2_3-GSM929150.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/msl3_1-GSM929151.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/msl3_1-GSM929151.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/msl3_1-GSM929151.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 36-MSL-GSE37864/msl3_2-GSM929152.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 36-MSL-GSE37864/msl3_2-GSM929152.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 36-MSL-GSE37864/msl3_2-GSM929152.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 37-MCM-GSE28065/MCM_S2_July_2010_extraction1_seq1_aliquote_1-GSM694120.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 37-MCM-GSE28065/MCM_S2_July_2010_extraction1_seq1_aliquote_1-GSM694120.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 37-MCM-GSE28065/MCM_S2_July_2010_extraction1_seq1_aliquote_1-GSM694120.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 37-MCM-GSE28065/MCM_S2_July_2010_extraction2_seq1_aliquote_1-GSM694121.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 37-MCM-GSE28065/MCM_S2_July_2010_extraction2_seq1_aliquote_1-GSM694121.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 37-MCM-GSE28065/MCM_S2_July_2010_extraction2_seq1_aliquote_1-GSM694121.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 38-CTCF_CP190-GSE96581/CP190_ChIP-seq-GSM2536237.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 38-CTCF_CP190-GSE96581/CP190_ChIP-seq-GSM2536237.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 38-CTCF_CP190-GSE96581/CP190_ChIP-seq-GSM2536237.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 38-CTCF_CP190-GSE96581/CTCF_ChIP-seq-GSM2536239.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 38-CTCF_CP190-GSE96581/CTCF_ChIP-seq-GSM2536239.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 38-CTCF_CP190-GSE96581/CTCF_ChIP-seq-GSM2536239.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 38-CTCF_CP190-GSE96581/FLAG_ChIP-seq-GSM2536241.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 38-CTCF_CP190-GSE96581/FLAG_ChIP-seq-GSM2536241.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 38-CTCF_CP190-GSE96581/FLAG_ChIP-seq-GSM2536241.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 39-Pho-GSE84502/Pho-GSM2238595.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 39-Pho-GSE84502/Pho-GSM2238595.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 39-Pho-GSE84502/Pho-GSM2238595.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep1-GSM2521732.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep1-GSM2521732.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep1-GSM2521732.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep2-GSM2521733.36mers.unique.MACS-2.1.0_peaks.narrowPeak 0 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep2-GSM2521733.36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/dm6/dm6.chrom.sizes 40-ATAC-seq-GSE95689/S2_T0_H3K27ac_ChIP_rep2-GSM2521733.36mers.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM