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CCRGeneticsBranch / Oncogenomics_v2

Oncogenomics portal version 2
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ChIPseq pipeline rerun #64

Open hsienchao opened 2 months ago

hsienchao commented 2 months ago

We've decided to reorganize the old ChIPseq results by rerunning the old samples and merge them to the results processed by new pipeline (since Jun 2023). Then we can upload them to DB automatically. The results can be visualized on the web site. To achieve this, we need Jun/Young to fill the case name/project to the master file.

hsienchao commented 2 months ago

Update: I've finished 514 samples. Many of them were failed. This could be master file or FASTQ not found issues. I need to dig into this.

hsienchao commented 3 weeks ago
  1. Processed 814 samples.
  2. RNAseq failed due to OEL upgrade of Biowulf. Coltron is not supported anymore.
  3. There are still 688 samples not found in master file. See the attachment
  4. Once the case name and project are filled in master file. I can start sync them to Frederick server and DB
  5. The paired input sample should not include "Sample_".

not_found_in_master.txt

hsienchao commented 3 weeks ago

10_CUTLL1_GSI_washout_H3K27Ac_C_SRR1019704 10_H82N_D_adh_D28_H3K27me3_C_HWJ55DRXX 11_CUTLL1_GSI_washout_H3K27Ac_C_SRR1019705 11_H82N_D_susp_D56_H3K27me3_C_HWJ55DRXX 12_CUTLL1_vehicle_MED1_C_SRR1019706 12_H82N_D_adh_D56_H3K27me3_C_HWJ55DRXX 13_CUTLL1_vehicle_P300_C_SRR1025396 13_H82_H3K27Ac_C_HWJ55DRXX 14_CUTLL1_vehicle_ETS1_C_SRR1202094 14_H82N_H3K27Ac_C_HWJ55DRXX 15_CUTLL1_vehicle_RUNX1_C_SRR1202094 15_H82N_D_susp_D28_H3K27Ac_C_HWJ55DRXX 16_H82N_D_adh_D28_H3K27Ac_C_HWJ55DRXX 17787N_H3K27ac_combined 17_H82N_D_susp_D56_H3K27Ac_C_HWJ55DRXX 1840_primary_H3K27ac_C_GSE128745 18481N_H3K27ac_combined 18810N_H3K27ac_combined 18_H82N_D_adh_D56_H3K27Ac_C_HWJ55DRXX 1_CUTLL1_vehicle_GABPA_C_SRR1019695 1_H82_H3K4me3_C_HWJ55DRXX 1_H82_IgG_control_S1_C_HTY7VBGXK 1_H82_S1_C_H55YNBGXK 20_H82N_ATAC_C_HWLWTDRXX 21_H82N_D_susp_D28_ATAC_C_HWLWTDRXX 2230_primary_H3K27ac_C_GSE128745 22_H82N_D_adh_D28_ATAC_C_HWLWTDRXX 23_H82N_D_susp_D56_ATAC_C_HWLWTDRXX 24_H82N_D_adh_D56_ATAC_C_HWLWTDRXX 293_C11orf95_r1_SBPtag_RK1_C_CRUK 293_C11orf95_r2_SBPtag_RK1_C_CRUK 293_C11orf95_r3_SBPtag_RK1_C_CRUK 293_Control_r1_SBPtag_RK1_C_CRUK 293_Control_r2_SBPtag_RK1_C_CRUK 293_Control_r3_SBPtag_RK1_C_CRUK 293_CR1_r1_SBPtag_RK1_C_CRUK 293_CR1_r2_SBPtag_RK1_C_CRUK 293_CR1_r3_SBPtag_RK1_C_CRUK 293_NT_Mock_RK1_C_CRUK 293_RELA_r1_SBPtag_RK1_C_CRUK 293_RELA_r2_SBPtag_RK1_C_CRUK 293_RELA_r3_SBPtag_RK1_C_CRUK 2_CUTLL1_GSI72_none_C_SRR1019696 2_H82N_H3K4me3_C_HWJ55DRXX 2_H82_NOTCH1_S2_C_HTY7VBGXK 2_H82N_S2_C_H55YNBGXK 3_CUTLL1_GSI72_NOTCH1_C_SRR1019697 3_H82N_D_susp_D28_H3K4me3_C_HWJ55DRXX 3_H82_NOTCH_ICD_S3_C_HTY7VBGXK 3_H82NplusD_D28_susp_S3_C_H55YNBGXK 434_primary_H3K27ac_C_GSE128745 4_CUTLL1_GSI72_RBPJ_C_SRR1019698 4_H82N_D_adh_D28_H3K4me3_C_HWJ55DRXX 4_H82_NOTCH2_S4_C_HTY7VBGXK 4_H82NplusD_D28_adh_S4_C_H55YNBGXK 5_CUTLL1_GSI72_washout_none_C_SRR1019699 5_H82N_D_susp_D56_H3K4me3_C_HWJ55DRXX 5_H82_NOTCH3_S5_C_HTY7VBGXK 6_CUTLL1_GSI_washout_NOTCH1_C_SRR1019700 6_H82N_D_adh_D56_H3K4me3_C_HWJ55DRXX 6_H82NplusD_D56_adh_S5_C_H55YNBGXK 6_H82_RBPJ_S6_C_HTY7VBGXK 7_CUTLL1_GSI_washout_RBPJ_C_SRR1019701 7_H82_H3K27me3_C_HWJ55DRXX 7_H82_REST_S7_C_HTY7VBGXK 8_CUTLL1_vehicle_H3K27Ac_C_SRR1019702 8_H82N_H3K27me3_C_HWJ55DRXX 9_CUTLL1_GSI_H3K27Ac_C_SRR1019703 9_H82N_D_susp_D28_H3K27me3_C_HWJ55DRXX A549_H3K27ac_SRR568435_C_GSE29611 A637_H3K27ac_1_CUTnTAG_C_GSE144651 A637_H3K27ac_2_CUTnTAG_C_GSE144651 A673_48shFLI1_FLI1_C_SRR1593995 A673_48shFLI1_H3K27ac_C_SRR1593996 A673_48shGFP_FLI1_C_SRR1593992 A673_48shGFP_H3K27ac_C_SRR1593993 A673_96shFLI1_H3K27ac_C_SRR1593997 A673_96shGFP_H3K27ac_C_SRR1593994 A673_ESW-FLI1_C_SRR13577547_GSE165783 A673_FLI1_C_SRR1593985 A673_H3K27ac_C_SRR1593986 A673_H3K27me3_C_SRR1593988 A673_H3K4me1_C_SRR1593987 A673_H3K4me3_C_SRR1593989 A673_STAG2ko_ESW-FLI1_C_SRR13577550_GSE165783 A673_STAG2ko_H3K27me3_C_SRR14333718_GSE165783 A673_STAG2ko_STAG1_C_SRR13577552_GSE165783 A673_STAG2ko_STAG2_C_SRR13577554_GSE165783 A673_STAG2null_H3K27ac_C_SRR14546338_GSE165783 A673_STAG2wt_ESW-FLI1_C_SRR13577549_GSE165783 A673_STAG2wt_H3K27ac_C_SRR14546336_GSE165783 A673_STAG2wt_H3K4me3_C_SRR14333719_GSE165783 A673_STAG2wt_SMC1A_C_SRR13577555_GSE165783 A673_STAG2wt_SMC1A_SRR13577555_C_GSE165783 A673_STAG2wt_STAG1_C_SRR13577551_GSE165783 A673_STAG2wt_STAG2_C_SRR13577553_GSE165783 A673_WCE_C_SRR1593991 A673_WDR5_C_SRR1593990 ANBL6-1XIL6_DHS_C_WK2 ANBL6-1X-IL6_DHS_C_WK3 ANBL6-5X-IL6_DHS_C_WK2 ANBL6-IL6_DHS_C_WK2 Bcell_ATAC_SRR2920492_C_GSE74912 Bcell_ATAC_SRR2920513_C_GSE74912 Bcell_ATAC_SRR2920517_C_GSE74912 Bcell_H3K27ac_SRR568215_C_GSE29611 Bcell_H3K27ac_SRR568216_C_GSE29611 Bcell_H3K27ac_SRR609630_C_GSE29611 Bcell_H3K27ac_SRR609631_C_GSE29611 BE2C_CTCF_C_SRR604578 BE2C_GATA3_C_SRR5249451 BE2C_HAND2_C_SRR5249436 BE2C_ISL1_C_SRR5249440 BE2C_MYCN_C_SRR5249439 BE2C_PHOX2B_C_SRR5249434 BE2C_TBX2_C_SRR5249442 BE2_H3K27ac_SRR2016192_C_GSE65664 Birch_H3K27ac_016_C_H5JKVBGX3 BT245_cell_H3K27ac_C_GSE128745 CART_JUNHAtag_IRF4_rep1_IRF4_SRR10067115_C_GSE136853 CART_JUNHAtag_IRF4_rep2_IRF4_SRR10067118_C_GSE136853 CART_JUNHAtag_JUN_rep1_Jun_SRR10067116_C_GSE136853 CART_JUNHAtag_JUN_rep2_Jun_SRR10067119_C_GSE136853 CD4_ATAC_SRR2920493_C_GSE74912 CD4_ATAC_SRR2920496_C_GSE74912 CD4_ATAC_SRR2920514_C_GSE74912 CD8_ATAC_SRR2920494_C_GSE74912 CD8_ATAC_SRR2920497_C_GSE74912 CD8_ATAC_SRR2920515_C_GSE74912 CLP_ATAC_SRR2920498_C_GSE74912 CLP_ATAC_SRR2920522_C_GSE74912 CLP_ATAC_SRR2920528_C_GSE74912 CM_CD8CD45ORposCD62Lhigh_ATAC_SRR4568589_C_GSE89308 CM_CD8CD45ORposCD62Lhigh_ATAC_SRR4568590_C_GSE89308 CM_CD8CD45ORposCD62Lhigh_ATAC_SRR4568591_C_GSE89308 CMP_ATAC_SRR2920469_C_GSE74912 CMP_ATAC_SRR2920481_C_GSE74912 CMP_ATAC_SRR2920500_C_GSE74912 CTR_CTCF_009_C_HHC7KBGXX CTR_D48_E2A_005_C_H7WKVBGXX CTR_D48_ERK_004_C_HH7C5BGXX CTR_D48_ERKabc_010_C_HMKGLBGXX CTR_D48_ERKmp_010_C_HMKGLBGXX CTR_D48_ERKmp_010_C_HMKGLBGXX_test CTR_D48_EZH2_004_C_HH7C5BGXX CTR_D48_H3K27ac_010_C_HMKGLBGXX CTR_D48_H3K27me3_010_C_HMKGLBGXX CTR_D48_H3K36me3_004_C_HH7C5BGXX CTR_D48_H3K4me3_004_C_HH7C5BGXX CTR_D48_MYOD1_002_C_HCK7HBGXX CTR_D48_MYOG_010_C_HMKGLBGXX CTR_D48_Pol2_S2p_018_C_HWC77BGXY CTR_D48_Pol2S2pAC_025_C_HFH72BGX5 CTR_D48_Pol2S2pAMR_025_C_HFH72BGX5 CTR_D48_Pol2_S5p_018_C_HWC77BGXY CTR_D48_PolII_010_C_HMKGLBGXX CTR_D48_SNAI2_031_CM_H3HYNBGX7_HGY5YBGX7 CTR_DMSO_SUZ12_011_C_HF7LLBGXY CTR_ERK_002_C_HCK7HBGXX CTR_H3K27ac_001_C_H5TLGBGXX CTR_H3K27me3_001_C_H5TLGBGXX CTR_H3K4me1_002_C_HCK7HBGXX CTR_H3K4me2_002_C_HCK7HBGXX CTR_HDAC2_008_C_HHC7JBGXX CTR_MYC_001_C_H5TLGBGXX CTR_MYOD1_001_C_H5TLGBGXX CTR_rep1_H3K27ac_HiChIP_HVHLGBGXB CTR_rep3_H3K27ac_HiChIP_HVHLGBGXB CTR_rep6_H3K27ac_HiChIP_HVHT2BGXB CTR_rep7_H3K27ac_HiChIP_HVHT2BGXB CTR_rep8_H3K27ac_HiChIP_HVHT2BGXB CTR_T48_E2A_005_C_H7WKVBGXX CTR_T48_ERK_004_C_HH7C5BGXX CTR_T48_ERKabc_010_C_HMKGLBGXX CTR_T48_ERKmp_010_C_HMKGLBGXX CTR_T48_ERKmp_010_C_HMKGLBGXX_test CTR_T48_EZH2_004_C_HH7C5BGXX CTR_T48_H3K27ac_002_C_HCK7HBGXX CTR_T48_H3K27ac_010_C_HMKGLBGXX CTR_T48_H3K27me3_004_C_HH7C5BGXX CTR_T48_H3K27me3_010_C_HMKGLBGXX CTR_T48_MYOD1_002_C_HCK7HBGXX CTR_T48_MYOG_010_C_HMKGLBGXX CTR_T48_Pol2_S2p_018_C_HWC77BGXY CTR_T48_Pol2S2pAC_025_C_HFH72BGX5 CTR_T48_Pol2S2pAMR_025_C_HFH72BGX5 CTR_T48_Pol2_S5p_018_C_HWC77BGXY CTR_T48_PolII_010_C_HMKGLBGXX CTR_T48_SNAI2_031_CM_H3HYNBGX7_HGY5YBGX7 CTR_Tram_SUZ12_011_C_HF7LLBGXY DLD1_ATF4_SRR7532398_C_GEO DLD1_ATF4_SRR7532399_C_GEO DLD1_OHT-MYC_ATF4_SRR7532400_C_GEO DLD1_OHT-MYC_ATF4_SRR7532401_C_GEO DLD1_OHT-MYC_MYC_SRR7532402_C_GEO DLD1_OHT-MYC_MYC_SRR7532403_C_GEO DND41_H3K27ac_SRR568222_C_GSE29611 DonorPB1804_TGFB_6h_ATAC_C_AAAT5LGHV DonorPB1804_Veh_6h_ATAC_C_AAAT5LGHV EM_CD8CD45ROposCD62Llow_ATAC_SRR4568586_C_GSE89308 EM_CD8CD45ROposCD62Llow_ATAC_SRR4568587_C_GSE89308 EM_CD8CD45ROposCD62Llow_ATAC_SRR4568588_C_GSE89308 Endoderm_SMAD2and3_RepB_SRR212461_C_GSE29422 Erythroblast_ATAC_SRR2920502_C_GSE74912 Erythroblast_ATAC_SRR2920523_C_GSE74912 Erythroblast_ATAC_SRR2920529_C_GSE74912 Exh_CD8PDL1hi_MELpt1_ATAC_SRR4568592_C_GSE89308 Exh_CD8PDL1hi_MELpt2_ATAC_SRR4568593_C_GSE89308 Exh_CD8PDL1hi_NSCLCpt1_ATAC_SRR4568594_C_GSE89308 G477_cell_H3K27ac_C_GSE128745 GMP_ATAC_SRR2920471_C_GSE74912 GMP_ATAC_SRR2920483_C_GSE74912 GMP_ATAC_SRR2920505_C_GSE74912 H929-2_H3K27ac_CWK9 H929_DHS_C_WK1 HCT116_H3K27ac_SRR507800_C_GSE38447 HCT116_H3K27ac_SRR969189_C_GSE50610 HEK293T_H3K27ac_SRR1016003_C_GSE51633 HepG2_H3K27ac_SRR227575_C_GSE51334 hESC_SMAD2and3_RepB_SRR212442_C_GSE29422 hMSC_ATF4_SRR2025080_C_GEO HSC_ATAC_SRR2920466_C_GSE74912 HSC_ATAC_SRR2920477_C_GSE74912 HSC_ATAC_SRR2920506_C_GSE74912 HUVEC_H3K27ac_SRR882022_C_GSE43070 IMR90_Grow_RB_SRR034479_C_GSE19898 IMR90_H3K27ac_SRR639067_C_GSE43070 IMR90_Senes_RB_SRR034485_C_GSE19898 JN29_primary_H3K27ac_C_GSE128745 Jurkat_SMAD_TGFb_1ng_6h_IgG_Epicy_CUTnRUN_C_HLVMMBGXM K562_ATF4_SRR8660104_C_GEO K562_CTCF_1_CUTnTAG_C_GSE124557 K562_CTCF_2_CUTnTAG_C_GSE124557 K562_H3K27ac_1_CUTnTAG_C_GSE124557 K562_H3K27ac_2_CUTnTAG_C_GSE124557 K562_Run2_CTCF_SRR227524_C_GSE51334 KCNR_2D_C_H3K27ac_C_HLL3CBGXX KCNR_2D_RA_H3K27ac_C_HLL3CBGXX KCNR_4D_C_H3K27ac_C_HLL3CBGXX KCNR_4D_C_H3K4me1_CS024461_C_H2NYCBGXB KCNR_4D_C_H3K4me3_CS024461_C_H2NYCBGXB KCNR_4D_C_IgG_MWZ_C_MWZ8588 KCNR_4D_C_SOX11_Abc_MWZ_C_MWZ8588 KCNR_4D_C_SOX11_CS024461_C_H2NYCBGXB KCNR_4D_C_SOX11_CS024724_C_H7TFVBGXB KCNR_4D_C_SOX11_Sig_MWZ_C_MWZ8588 KCNR_4D_C_SOX4_CS024724_C_H7TFVBGXB KCNR_4D_C_SOX4_MWZ_C_MWZ8588 KCNR_4D_RA_H3K27ac_C_HLL3CBGXX KCNR_4D_RA_H3K4me1_CS024461_C_H2NYCBGXB KCNR_4D_RA_H3K4me3_CS024461_C_H2NYCBGXB KCNR_4D_RA_IgG_MWZ_C_MWZ8588 KCNR_4D_RA_SOX11_Abc_MWZ_C_MWZ8588 KCNR_4D_RA_SOX11_CS024461_C_H2NYCBGXB KCNR_4D_RA_SOX11_CS024724_C_H7TFVBGXB KCNR_4D_RA_SOX11_Sig_MWZ_C_MWZ8588 KCNR_4D_RA_SOX4_CS024724_C_H7TFVBGXB KCNR_4D_RA_SOX4_MWZ_C_MWZ8588 KCNR_8D_C_H3K27ac_C_HLL3CBGXX KCNR_8D_RA_H3K27ac_C_HLL3CBGXX KCNR_C1_EZH2_C_C67CBANXX KCNR_rep2_4D_CTL_IgG_C_MWZ8711 KCNR_rep2_4D_CTL_SOX11_Abc_C_MWZ8711 KCNR_rep2_4D_CTL_SOX11_Sig_C_MWZ8711 KCNR_rep2_4D_CTL_SOX4_C_MWZ8711 KCNR_rep2_4D_RA_IgG_C_MWZ8711 KCNR_rep2_4D_RA_SOX11_Abc_C_MWZ8711 KCNR_rep2_4D_RA_SOX11_Sig_C_MWZ8711 KCNR_rep2_4D_RA_SOX4_C_MWZ8711 Kelly_GATA3_SRR1790658_C_GSE65664 KG1_CREB-BP_C_SRR2919453 KHM11_DHS_C_WK2 KHM11_DHS_C_WK3 KP6_DHS_C_WK1 KP6_DHS_C_WK2 KP6_DHS_C_WK3 LAN5_2D_C_H3K27ac_CCRSF004_C_HTLNHBGX7 LAN5_2D_RA_H3K27ac_CCRSF004_C_HTLNHBGX7 LAN5_4D_C_H3K27ac_CCRSF004_C_HTLNHBGX7 LAN5_4D_RA_H3K27ac_CCRSF004_C_HTLNHBGX7 LAN5_8D_C_H3K27ac_CCRSF004_C_HTLNHBGX7 LAN5_8D_RA_H3K27ac_CCRSF004_C_HTLNHBGX7 LMPP_ATAC_SRR2920468_C_GSE74912 LMPP_ATAC_SRR2920480_C_GSE74912 LMPP_ATAC_SRR2920535_C_GSE74912 LNCaP_512_lowMYC_MYC_C_SOW LNCaP_627_lowMYC_MYC_C_SOW LNCaP_637_lowMYC_MYC_C_SOW LNCaP_Bic1_AR_SRR999224_C_GSE43791 LNCaP_Bic2_AR_SRR999225_C_GSE43791 LNCaP_control_H3K27ac_CS023273_C_DVW LNCaP_Ctrl_HighMYC_MYC_C_SOW LNCaP_DHT_exo1_AR_SRR653219_C_GSE43791 LNCaP_DHT_exo2_AR_SRR653220_C_GSE43791 LNCaP_DHT_FOXA1_SRR652256_C_GSE43791 LNCaP_Enza1_AR_SRR999228_C_GSE43791 LNCaP_Enza2_AR_SRR999229_C_GSE43791 LNCaP_R1881_AR_SRR5104232_C_GSE92347 LNCaP_R1881_AR_SRR5238075_C_GSE94682 LNCaP_V1_AR_SRR653091_C_GSE43791 LNCaP_V1_H3K27me3_SRR653093_C_GSE43791 LNCaP_V1_H3K4me1_SRR653095_C_GSE43791 LNCaP_V1_H3K4me2_SRR653097_C_GSE43791 LNCaP_V1_H3K4me3_SRR653099_C_GSE43791 LNCaP_V1_H3K9me3_SRR653101_C_GSE43791 LNCaP_V2_AR_SRR653092_C_GSE43791 LNCaP_V2_H3K27me3_SRR653094_C_GSE43791 LNCaP_V2_H3K4me1_SRR653096_C_GSE43791 LNCaP_V2_H3K4me2_SRR653098_C_GSE43791 LNCaP_V2_H3K4me3_SRR653100_C_GSE43791 LNCaP_veh_exo1_AR_SRR653215_C_GSE43791 LNCaP_veh_FOXA1_SRR652255_C_GSE43791 LNCaP_Veh_rep1_FOXA1_SRR5238084_C_GSE94682 LNCaP_WT_HighMYC_MYC_C_SOW LREX_DMSO_AR_CS023271_C_DVW LREX_DMSO_H3K27ac_CS023271_C_DVW LREX_Enza_Ipat_AR_CS023271_C_DVW LREX_Enza_Ipat_H3K27ac_CS023271_C_DVW LREX_Enzalutamide_AR_CS023271_C_DVW LREX_Enzalutamide_H3K27ac_CS023271_C_DVW LREX_Ipatasertib_AR_CS023271_C_DVW LREX_Ipatasertib_H3K27ac_CS023271_C_DVW LREX_R1881_AR_CS023271_C_DVW LREX_R1881_H3K27ac_CS023271_C_DVW LuCaP_136_AR_GSE130408 LuCaP136_combo1_AR_C_AAACNCNHV LuCaP136_combo1_H3K27ac_C_AAACNCNHV LuCaP136_combo2_AR_C_AAACNCNHV LuCaP136_combo2_H3K27ac_C_AAACNCNHV LuCaP136_ctrl1_AR_C_AAACNCNHV LuCaP136_ctrl1_H3K27ac_C_AAACNCNHV LuCaP136_ctrl2_AR_C_AAACNCNHV LuCaP136_ctrl2_H3K27ac_C_AAACNCNHV LuCaP136_dht1_AR_C_AAACNCNHV LuCaP136_dht1_H3K27ac_C_AAACNCNHV LuCaP136_dht2_AR_C_AAACNCNHV LuCaP136_dht2_H3K27ac_C_AAACNCNHV LuCaP136_enza1_AR_C_AAACNCNHV LuCaP136_enza1_H3K27ac_C_AAACNCNHV LuCaP136_enza2_AR_C_AAACNCNHV LuCaP136_enza2_H3K27ac_C_AAACNCNHV LuCaP_136_H3K27ac_GSE130408 LuCaP136_ipat1_AR_C_AAACNCNHV LuCaP136_ipat1_H3K27ac_C_AAACNCNHV LuCaP136_ipat2_AR_C_AAACNCNHV LuCaP136_ipat2_H3K27ac_C_AAACNCNHV LuCaP_141_AR_GSE130408 LuCaP_141_H3K27ac_GSE130408 LuCaP_167_AR_GSE130408 LuCaP_167_H3K27ac_GSE130408 LuCaP_170-2_AR_GSE130408 LuCaP_170-2_H3K27ac_GSE130408 LuCaP_170-3_AR_GSE130408 LuCaP_170-3_H3K27ac_GSE130408 LuCaP_189-3_AR_GSE130408 LuCaP_189-3_H3K27ac_GSE130408 LuCaP_189-4_AR_GSE130408 LuCaP_189-4_H3K27ac_GSE130408 LuCaP_35_AR_GSE130408 LuCaP_35_H3K27ac_GSE130408 LuCaP_58_AR_GSE130408 LuCaP_58_H3K27ac_GSE130408 LuCaP_70_AR_GSE130408 LuCaP_70_H3K27ac_GSE130408 LuCaP_77_AR_GSE130408 LuCaP_77_H3K27ac_GSE130408 LuCaP_78_AR_GSE130408 LuCaP_78_H3K27ac_GSE130408 LuCaP_81_AR_GSE130408 LuCaP_81_H3K27ac_GSE130408 LuCaP_82-2_H3K27ac_GSE130408 LuCaP_86-2_AR_GSE130408 LuCaP_92_AR_GSE130408 Lu_iPSC6_H3K27Me3_C_SRR5942340 Lu_iPSC6_H3K4Me3_C_SRR5942335 Lu_iPSC6_IgG_C_SRR5942341 Lu_iPSC7_H3K27Me3_C_SRR5942346 Lu_iPSC7_H3K4Me3_C_SRR5942343 Lu_iPSC7_IgG_C_SRR5942347 Mast118_H3K9ac_009_C_HHC7KBGXX Mast118_HDAC2_009_C_HHC7KBGXX Mast118_P3F_009_C_HHC7KBGXX MB231_ER_1_020_C_HCVW3BGX2 MB231_IgG_1_020_C_HCVW3BGX2 MB231_RecQ1_1_020_C_HCVW3BGX2 MCC13_H3K27ac_014_C_HJH7GBGXY MCC26_H3K27ac_014_C_HJH7GBGXY MCF7_CTCF_SRR7686901_C_GSE104983 MCF7_ER_1_020_C_HCVW3BGX2 MCF7_ER_2_020_C_HCVW3BGX2 MCF7_ETO_ENDseq_GSE99194 MCF7_H3K27ac_SRR507789_C_GSE38447 MCF7_IgG_1_020_C_HCVW3BGX2 MCF7_IgG_2_020_C_HCVW3BGX2 MCF7_NT_ENDseq_GSE99194 MCF7_RecQ1_1_020_C_HCVW3BGX2 MCF7_RecQ1_2_020_C_HCVW3BGX2 MDAMB231_TGFB_1h_SMAD3_SRR5113705_C_GSE92443 MEP_ATAC_SRR2920473_C_GSE74912 MEP_ATAC_SRR2920485_C_GSE74912 MEP_ATAC_SRR2920508_C_GSE74912 MKL1_ATOH1_027_C_HTK33BBXX MKL1_H3K27ac_014_C_HJH7GBGXY MKL1_INSM1_027_C_HTK33BBXX MKL1_ISL1_027_C_HTK33BBXX MKL1_LXH3_027_C_HTK33BBXX MKL1_POU4F3_027_C_HTK33BBXX MKL1_SOX2_027_C_HTK33BBXX MKL2_ATOH1_027_C_HTK33BBXX MKL2_H3K27ac_014_C_HJH7GBGXY MKL2_INSM1_027_C_HTK33BBXX MKL2_ISL1_027_C_HTK33BBXX MKL2_LXH3_027_C_HTK33BBXX MKL2_POU4F3_027_C_HTK33BBXX MKL2_SOX2_027_C_HTK33BBXX MM1S_CDK7_SRR825494_C_JQ MM1S_CDK9_SRR748842_C_JQ MM1S_DMSO_H3K4me3_DFCI_C_JQ MM1S_DMSO_H3K4me3_DFCI_Rx_C_JQ MM1S_DMSO_KDM5A_DFCI_C_JQ MM1S_DMSO_Pol2_DFCI_C_JQ MM1S_DMSO_Pol2_DFCI_Rx_C_JQ MM1S_DMSO_Pol2_S2p_DFCI_C_JQ MM1S_DMSO_Pol2_S5p_DFCI_C_JQ MM1S_empty_DMSO_Pol2_ser5_Rx_C_JQ MM1S_empty_JQKD82_Pol2_ser5_Rx_C_JQ MM1S_JQKD82_H3K4me3_DFCI_C_JQ MM1S_JQKD82_H3K4me3_DFCI_Rx_C_JQ MM1S_JQKD82_KDM5A_DFCI_C_JQ MM1S_JQKD82_Pol2_DFCI_C_JQ MM1S_JQKD82_Pol2_DFCI_Rx_C_JQ MM1S_JQKD82_Pol2_S2p_DFCI_C_JQ MM1S_JQKD82_Pol2_S5p_DFCI_C_JQ MM1S_MYC_DMSO_Pol2_ser5_Rx_C_JQ MM1S_MYC_JQKD82_Pol2_ser5_Rx_C_JQ MM1S_MYC_SRR444479_C_JQ MM1S_NT_KDM5A_DFCI_C_JQ MM1S_shKDM5A_H3K4me3_DFCI_Rx_C_JQ MM1S_shKDM5A_Pol2_DFCI_Rx_C_JQ MM1S_shLuc_H3K4me3_DFCI_Rx_C_JQ MM1S_shLuc_Pol2_DFCI_Rx_C_JQ MM-M1_IRF4_C_WK7_bk_20180327 mm_Myoblasts_Myod_C_GSE63716 mm_Myoblasts_rep1_H3K27ac_C_GSE37525 mm_Myoblasts_rep1_p300_C_GSE37525 mm_Myoblasts_rep1_PolII_C_GSE25308 mm_Myotubes_Myod_C_GSE63716 mm_Myotubes_rep1_H3K27ac_C_GSE37525 mm_Myotubes_rep1_p300_C_GSE37525 mm_Myotubes_rep1_PolII_C_GSE25308 MOLM13_CDK9_SRR3465901_C_GSE80779 MOLM13_H3K27ac_SRR3465906_C_GSE80779 MOLM13_H3K79me2_SRR7010333_C_GSE113191 MOLM13_POL2_SRR3465911_C_GSE80779 MOLM13_SMARCA4_SRR6987864_C_GSE113042 MOLM14_H3K27ac_024_C_HLFMLBGX3trim Monocyte_ATAC_SRR2920475_C_GSE74912 Monocyte_ATAC_SRR2920487_C_GSE74912 Monocyte_ATAC_SRR2920542_C_GSE74912 MPP_ATAC_SRR2920467_C_GSE74912 MPP_ATAC_SRR2920479_C_GSE74912 MPP_ATAC_SRR2920509_C_GSE74912 MS1_H3K27ac_014_C_HJH7GBGXY murPRAMETCR_TIL_dnTGFBR2_D10_Rep1_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_dnTGFBR2_D10_Rep1_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_dnTGFBR2_D10_Rep2_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_dnTGFBR2_D10_Rep2_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_dnTGFBR2_D10_Rep3_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_dnTGFBR2_D10_Rep3_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_dnTGFBR2_D10_Rep4_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_dnTGFBR2_D10_Rep4_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_tEGFR_D10_Rep1_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_tEGFR_D10_Rep1_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_tEGFR_D10_Rep2_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_tEGFR_D10_Rep2_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_tEGFR_D10_Rep3_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_tEGFR_D10_Rep3_ATAC_C_HLVVNBGXM murPRAMETCR_TIL_tEGFR_D10_Rep4_ATAC_C2_HMW7HBGXN murPRAMETCR_TIL_tEGFR_D10_Rep4_ATAC_C_HLVVNBGXM MusclePs_H3K27ac_C_SRR1045535 MusclePs_H3K27ac_C_SRR1045536 MusclePs_H3K27ac_C_SRR1045537 Naive_CD8CD45RApos_ATAC_SRR4568583_C_GSE89308 Naive_CD8CD45RApos_ATAC_SRR4568584_C_GSE89308 Naive_CD8CD45RApos_ATAC_SRR4568585_C_GSE89308 Nalm6_ETO_ENDseq_GSE99194 Nalm6_NT_ENDseq_GSE99194 NB4_FLI1_C_SRR401269 NCI0075_H3K27ac_007_C_HHF57BGXX NCI0082_H3K27ac_007_C_HHF57BGXX NILC_BRD4_004_C_HH7C5BGXX NILC_H3K27ac_004_C_HH7C5BGXX NILC_P3F_010_C_HMKGLBGXX Nkcell_ATAC_SRR2920495_C_GSE74912 Nkcell_ATAC_SRR2920511_C_GSE74912 Nkcell_ATAC_SRR2920516_C_GSE74912 no4c2_RH4_H3K36me3_005_C_H7WKVBGXX no4c_RH4_H3K36me3_005_C_H7WKVBGXX no4c_RH4_H3K9me2_005_C_H7WKVBGXX NS129_H3K27ac_007_C_HHF57BGXX NS134_H3K27ac_007_C_HHF57BGXX OCI-LY1_CTCF_SRR8275089_C_GSE123200 OCI-LY3_CTCF_SRR8275136_C_GSE123225 PANC1_2_H3K27ac_SRR353689_C_GSE31755 PANC1_H3K27ac_SRR353688_C_GSE31755 PCa_M1_exo1_AR_SRR653227_C_GSE43791 PCa_M1_exo1_AR_SRR653228_C_GSE43791 PCa_M2_exo1_AR_SRR653229_C_GSE43791 PCa_M3_exo2_AR_SRR653232_C_GSE43791 PCa_M4_exo1_AR_SRR653233_C_GSE43791 PCa_M4_exo2_AR_SRR653234_C_GSE43791 PCa_N1_exo1_AR_SRR653223_C_GSE43791 PCa_N1_exo2_AR_SRR653224_C_GSE43791 PCa_N2_exo1_AR_SRR653225_C_GSE43791 PCa_N2_exo2_AR_SRR653226_C_GSE43791 PCaTumor16_AR_SRR1206265_C_GSE70079 PCaTumor17_AR_SRR1206266_C_GSE70079 PCaTumor18_AR_SRR1206267_C_GSE70079 PF19_BRD4_004_C_HH7C5BGXX PF19_H3K27ac_004_C_HH7C5BGXX PF19_P3F_010_C_HMKGLBGXX Raji_H3K27ac_SRR1201297_C_GSE52914 Raji_H3K4me3_SRR1041782_C_GSE52914 Raji_Pol2_SRR1041784_C_GSE52914 Raji_ssDNA_combined_C_SRP020626 RD_24h_DM_MYOD_SRR959021_C_GSE50413 RD_H3K27ac_008_C_HHC7JBGXX RD_HDAC2_008_C_HHC7JBGXX RD_shCtrl_DM_H3K27ac_L007_C_UTHSCSA RD_shCtrl_DM_MYOD_L007_C_UTHSCSA RD_shCtrl_DM_SNAI2_L007_C_UTHSCSA RD_shSNAI2_DM_H3K27ac_L007_C_UTHSCSA RD_shSNAI2_DM_MYOD_L007_C_UTHSCSA RD_shSNAI2_DM_SNAI2_L007_C_UTHSCSA RH18_H3K27ac_009_C_HHC7KBGXX RH18_MYF5_009_C_HHC7KBGXX RH30_H3K27ac_016_C_H5JKVBGX3 RH3_H3K27ac_016_C_HJ73HBGXY RH3_P3F_016_C_HJ73HBGXY RH4_2_CTCF_008_C_HHC7JBGXX RH4_BRD9_200413_C_BZS RH4_CHD4m_005_C_H7WKVBGXX RH4_CHD4_nFlag_018_C_HWC77BGXY RH4_CHD4p_005_C_H7WKVBGXX RH4_CTCF_008_C_HHC7JBGXX RH4_CUTnRUN4_IgG_ab1 RH4_CUTnRUN4_NFYB_ab1RM RH4_CUTnRUN4_NFYC_ab1RM RH4_CUTnRUN5_IgG_ab1 RH4_CUTnRUN5_NFYB_ab2Inv RH4_D6_bioJQ1_016_C_HJ73HBGXY RH4_D6_bioMerck_024_C_HLFMLBGX3 RH4_D6_BRD4_004_C_HH7C5BGXX RH4_D6_BRD4_011_C_HLM7NBGXX RH4_D6_BRD4_024_C_HLFMLBGX3 RH4_D6_BRD4_P3F_011_C_HLM7NBGXX RH4_D6_H3K27ac_018_C_HWC77BGXY RH4_D6_H3K27ac_HiChIP_HH3JVBGX7 RH4_D6_H3K27ac_HiChIP_HKJ22BGX7 RH4_D6_HDAC1_024_C_HLFMLBGX3 RH4_D6_p300_024_C_HLFMLBGX3 RH4_D6_P3F_011_C_HLM7NBGXX RH4_D6_P3F_BRD4_011_C_HLM7NBGXX RH4_D6_Pol2_018_C_HWC77BGXY RH4_D6_RAD21_025_C_HFH72BGX5 RH4_D6_YY1_025_C_HFH72BGX5 RH4_DMSO_IgG_CUTnRUN_C_AAAT2LMHV RH4_DPF2_200413_C_BZS RH4_Ent1_H3K27ac_018_C_HWC77BGXY RH4_Ent1_Pol2_018_C_HWC77BGXY RH4_Ent6_bioMerck_024_C_HLFMLBGX3 RH4_Ent6_BRD4_024_C_HLFMLBGX3 RH4_Ent6_H3K27ac_018_C_HWC77BGXY RH4_Ent6_H3K27ac_HiChIP_HH3JVBGX7 RH4_Ent6_H3K27ac_HiChIP_HKJ22BGX7 RH4_Ent6_p300_024_C_HLFMLBGX3 RH4_Ent6_Pol2_018_C_HWC77BGXY RH4_Ent6_RAD21_025_C_HFH72BGX5 RH4_Ent6_YY1_025_C_HFH72BGX5 RH4_EZH2_018_C_HWC77BGXY RH4_Flag_018_C_HWC77BGXY RH4_FOXO1_CTCF2_009_4C_HHC7KBGXX RH4_H3K27ac_001_C_H5TLGBGXX RH4_H3K27me3_001_C_H5TLGBGXX RH4_H3K36me3_005_C_H7WKVBGXX RH4_H3K36me3_005_C_RM4CTEST RH4_H3K4me1_002_C_HCK7HBGXX RH4_H3K4me2_001_C_H5TLGBGXX RH4_H3K4me3_001_C_H5TLGBGXX RH4_H3K9_005_C_H7WKVBGXX RH4_H3K9ac_005_C_H7WKVBGXX RH4_H3K9me1_005_C_H7WKVBGXX RH4_H3K9me2_005_C_H7WKVBGXX RH4_H3K9me3_005_C_H7WKVBGXX RH4_HDAC2_005_C_H7WKVBGXX RH4_IgG_Epicy_CUTnRUN_C_HLVMMBGXM RH4_J6_BRD4_004_C_HH7C5BGXX RH4_J6_BRD4_011_C_HLM7NBGXX RH4_J6_BRD4_P3F_011_C_HLM7NBGXX RH4_J6hi_bioJQ1_016_C_HJ73HBGXY RH4_J6lo_bioJQ1_016_C_HJ73HBGXY RH4_J6_P3F_011_C_HLM7NBGXX RH4_J6_P3F_BRD4_011_C_HLM7NBGXX RH4_MED_002_C_HCK7HBGXX RH4_MYCN_002_C_HCK7HBGXX RH4_MYOD1_001_C_H5TLGBGXX RH4_MYOG_002_C_HCK7HBGXX RH4_p300SC_002_C_HCK7HBGXX RH4_PAX3FOXO1_SRR.32.35_C_Combined RH4_RAD21_008_C_HHC7JBGXX RH4_RBBP4_008_C_HHC7JBGXX RH4scr_P3F_008_C_HHC7JBGXX RH4sh404_48_P3F_009_C_HHC7KBGXX RH4_shBRD4_BRD4_011_C_HF7LLBGXY RH4_shBRD4_P3F_011_C_HF7LLBGXY RH4_shC_BRD4_011_C_HF7LLBGXY RH4shCHD4_72_P3F_005_C_H7WKVBGXX RH4_shC_P3F_011_C_HF7LLBGXY RH4shP3F_48_P3F_009_C_HHC7KBGXX RH4shP3F_72_P3F_005_C_H7WKVBGXX RH4_shP3F_BRD4_011_C_HF7LLBGXY RH4shP3F_H3K27ac_016_C_HJ73HBGXY RH4shscr_48_P3F_009_C_HHC7KBGXX RH4shscr_72_P3F_005_C_H7WKVBGXX RH4shScram_H3K27ac_016_C_HJ73HBGXY RH4_shScr_BRD4_011_C_HF7LLBGXY RH4_SOX8_016_C_HJ73HBGXY RH4_SUZ12_018_C_HWC77BGXY RH4_t6_BRD4_002_C_HCK7HBGXX RH5_H3K27ac_008_C_HHC7JBGXX RH5_HDAC2_008_C_HHC7JBGXX RH5_P3F_008_C_HHC7JBGXX RMS008_H3K27ac_007_C_HHF57BGXX RMS206_H3K27ac_007_C_HHF57BGXX RMS209_H3K27ac_007_C_HHF57BGXX RMS216_H3K27ac_007_C_HHF57BGXX RMS237_H3K27ac_007_C_HHF57BGXX RMS238_H3K27ac_007_C_HHF57BGXX SAEC_H3K27Me3_C_SRR5942348 SAEC_H3K4Me3_C_SRR5942351 SAEC_IgG_C_SRR5942349 SCLC_GLC16_H3K27ac_SRR1613964_C_GSE62412 SCLC_H82_H3K27ac_SRR1613966_C_GSE62412 SCMC_H3K27ac_008_C_HHC7JBGXX SCMC_HDAC2_008_C_HHC7JBGXX SCMC_P3F_016_C_HJ73HBGXY skMC_H3K27ac_021_C_H5JKVBGX3 SKMNC_48shFLI1_FLI1_C_SRR1593976 SKMNC_48shFLI1_H3K27ac_C_SRR1593977 SKMNC_48shGFP_FLI1_C_SRR1593967 SKMNC_48shGFP_H3K27ac_C_SRR1593968 SKMNC_96shFLI1_ELF1_C_SRR1593983 SKMNC_96shFLI1_FLI1_C_SRR1593978 SKMNC_96shFLI1_GABPA_C_SRR1593982 SKMNC_96shFLI1_H3K27ac_C_SRR1593979 SKMNC_96shFLI1_H3K27me3_C_SRR1593981 SKMNC_96shFLI1_H3K4me1_C_SRR1593980 SKMNC_96shFLI1_p300_C_SRR1593984 SKMNC_96shGFP_ELF1_C_SRR1593974 SKMNC_96shGFP_FLI1_C_SRR1593969 SKMNC_96shGFP_GABPA_C_SRR1593973 SKMNC_96shGFP_H3K27ac_C_SRR1593970 SKMNC_96shGFP_H3K27me3_C_SRR1593972 SKMNC_96shGFP_H3K4me1_C_SRR1593971 SKMNC_96shGFP_p300_C_SRR1593975 SKMNC_FLI1_C_SRR1593960 SKMNC_H3K27ac_C_SRR1593961 SKMNC_H3K27me3_C_SRR1593963 SKMNC_H3K4me1_C_SRR1593962 SKMNC_H3K4me3_C_SRR1593964 SKMNC_WCE_C_SRR1593966 SKMNC_WDR5_C_SRR1593965 SKNAS_ERK_021_C_H5JKVBGX3 SKNMC_BAF155_C_SRR5217613 SK-N-SH_CTCF_C_SRR3099537 SK-N-SH_CTCF_C_SRR568184 SU_DIPG_IV_H3K27ac_C_GSE94259 SU_DIPG_VI_H3K27ac_C_GSE94259 SU_DIPG_XIII_H3K27ac_C_GSE128745 SU_DIPG_XIIIP_H3K27ac_C_GSE94259 SU_DIPG_XVII_H3K27ac_C_GSE94259 supcGBM2_H3K27ac_C_GSE128745 THP-1_CTCF_SRR1177291_C_GSE55407 UAE_FLI1_C_SRR401270 UISO_H3K27ac_014_C_HJH7GBGXY VCaP_H3K27ac_C_SRR5345698 Waga_H3K27ac_014_C_HJH7GBGXY XG6_DHS_C_WK3

hsienchao commented 2 weeks ago

I worked with Young to figure out the potential reasons the runs failed. There are several categories:

  1. FASTQ file name is not ended with R1_fastq.gz
  2. FASTQ not found. (they will be ignored)
  3. 4C, Igg samples (they will be ignored)
  4. No FCID (Young has fixed them)
  5. Not found in master files (Young is still working on them)
  6. Matched normal has "Sample_". (Young has fixed them)
  7. SpikeIn genome not found. (We will use dm6)

As on 6/20, 1030 samples have been processed.

Jun should work on case/project definition in master files, so we can start uploading them to DB.

hsienchao commented 1 week ago

Finished 1327 cases. 159 cases remaining.