SeqMonk Vistory

Project Summary

Basic Project Info

ParameterValue
Project Namepluripotency_exit_DNMT_Epi_ChIP.smk
Vistory Namepluripotency_exit_DNMT_Epi_K27me3_pmQC.smv
GenomeMus musculus GRCm38_v95
SeqMonk Version1.46.0

Data Sets

NameFile NameReadsImport Options
ATAC_DNMT_KO_Epi_1Reimported from ATAC_DNMT_KO_Epi_17113690Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_Epi_2Reimported from ATAC_DNMT_KO_Epi_25547643Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_Epi_3Reimported from ATAC_DNMT_KO_Epi_35522265Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_1Reimported from ATAC_DNMT_KO_ES_16125661Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_2Reimported from ATAC_DNMT_KO_ES_25027523Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_KO_ES_3Reimported from ATAC_DNMT_KO_ES_35026670Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_1Reimported from ATAC_DNMT_WT_Epi_15413360Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_2Reimported from ATAC_DNMT_WT_Epi_24775153Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_Epi_3Reimported from ATAC_DNMT_WT_Epi_34936556Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_1Reimported from ATAC_DNMT_WT_ES_15973065Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_2Reimported from ATAC_DNMT_WT_ES_25012136Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
ATAC_DNMT_WT_ES_3Reimported from ATAC_DNMT_WT_ES_37445720Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_1Reimported from CTCF_DNMT_KO_Epi_123334028Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_2Reimported from CTCF_DNMT_KO_Epi_229180491Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_Epi_3Reimported from CTCF_DNMT_KO_Epi_325907443Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_1Reimported from CTCF_DNMT_KO_ES_118454754Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_2Reimported from CTCF_DNMT_KO_ES_221974831Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_KO_ES_3Reimported from CTCF_DNMT_KO_ES_322701344Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_1Reimported from CTCF_DNMT_WT_Epi_126298680Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_2Reimported from CTCF_DNMT_WT_Epi_220824648Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_Epi_3Reimported from CTCF_DNMT_WT_Epi_322115922Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_1Reimported from CTCF_DNMT_WT_ES_118591373Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_2Reimported from CTCF_DNMT_WT_ES_223250934Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
CTCF_DNMT_WT_ES_3Reimported from CTCF_DNMT_WT_ES_319583044Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_1Reimported from H3K27Ac_DNMT_KO_Epi_135150191Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_2Reimported from H3K27Ac_DNMT_KO_Epi_215686066Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_Epi_3Reimported from H3K27Ac_DNMT_KO_Epi_332506101Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_1Reimported from H3K27Ac_DNMT_KO_ES_125969291Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_2Reimported from H3K27Ac_DNMT_KO_ES_229683025Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_KO_ES_3Reimported from H3K27Ac_DNMT_KO_ES_326980378Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_1Reimported from H3K27Ac_DNMT_WT_Epi_128768816Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_2Reimported from H3K27Ac_DNMT_WT_Epi_224498898Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_Epi_3Reimported from H3K27Ac_DNMT_WT_Epi_319975962Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_1Reimported from H3K27Ac_DNMT_WT_ES_119220000Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_2Reimported from H3K27Ac_DNMT_WT_ES_225182652Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27Ac_DNMT_WT_ES_3Reimported from H3K27Ac_DNMT_WT_ES_325003296Visible stores parser Remove DuplicatesNo Downsample to approx 25000000
H3K27me3_DNMT_KO_Epi_1Reimported from H3K27me3_DNMT_KO_Epi_117404172Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_Epi_2Reimported from H3K27me3_DNMT_KO_Epi_218889750Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_Epi_3Reimported from H3K27me3_DNMT_KO_Epi_318764791Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_1Reimported from H3K27me3_DNMT_KO_ES_113753176Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_2Reimported from H3K27me3_DNMT_KO_ES_217595389Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_KO_ES_3Reimported from H3K27me3_DNMT_KO_ES_317142083Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_1Reimported from H3K27me3_DNMT_WT_Epi_117748539Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_2Reimported from H3K27me3_DNMT_WT_Epi_219673457Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_Epi_3Reimported from H3K27me3_DNMT_WT_Epi_315929372Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_1Reimported from H3K27me3_DNMT_WT_ES_119719565Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_2Reimported from H3K27me3_DNMT_WT_ES_218655219Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K27me3_DNMT_WT_ES_3Reimported from H3K27me3_DNMT_WT_ES_314377071Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_1Reimported from H3K4me1_DNMT_KO_Epi_127153874Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_2Reimported from H3K4me1_DNMT_KO_Epi_226355411Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_Epi_3Reimported from H3K4me1_DNMT_KO_Epi_323473276Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_ES_1Reimported from H3K4me1_DNMT_KO_ES_1390525529Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_ES_2Reimported from H3K4me1_DNMT_KO_ES_226186351Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_KO_ES_3Reimported from H3K4me1_DNMT_KO_ES_326314723Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_1Reimported from H3K4me1_DNMT_WT_Epi_124073496Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_2Reimported from H3K4me1_DNMT_WT_Epi_227935129Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_Epi_3Reimported from H3K4me1_DNMT_WT_Epi_328759185Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_1Reimported from H3K4me1_DNMT_WT_ES_123759911Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_2Reimported from H3K4me1_DNMT_WT_ES_228868709Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me1_DNMT_WT_ES_3Reimported from H3K4me1_DNMT_WT_ES_326527195Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_1Reimported from H3K4me3_DNMT_KO_Epi_120378459Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_2Reimported from H3K4me3_DNMT_KO_Epi_234087532Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_Epi_3Reimported from H3K4me3_DNMT_KO_Epi_329542675Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_1Reimported from H3K4me3_DNMT_KO_ES_132057373Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_2Reimported from H3K4me3_DNMT_KO_ES_228351839Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_KO_ES_3Reimported from H3K4me3_DNMT_KO_ES_325539542Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_1Reimported from H3K4me3_DNMT_WT_Epi_127309497Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_2Reimported from H3K4me3_DNMT_WT_Epi_227178120Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_Epi_3Reimported from H3K4me3_DNMT_WT_Epi_3286654573Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_1Reimported from H3K4me3_DNMT_WT_ES_138055549Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_2Reimported from H3K4me3_DNMT_WT_ES_232201989Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
H3K4me3_DNMT_WT_ES_3Reimported from H3K4me3_DNMT_WT_ES_336742727Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_1Reimported from Input_DNMT_KO_Epi_119707695Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_2Reimported from Input_DNMT_KO_Epi_220493345Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_Epi_3Reimported from Input_DNMT_KO_Epi_324969245Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_1Reimported from Input_DNMT_KO_ES_128680534Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_2Reimported from Input_DNMT_KO_ES_221088413Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_KO_ES_3Reimported from Input_DNMT_KO_ES_312203802Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_1Reimported from Input_DNMT_WT_Epi_128080334Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_2Reimported from Input_DNMT_WT_Epi_222301904Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_Epi_3Reimported from Input_DNMT_WT_Epi_320285377Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_1Reimported from Input_DNMT_WT_ES_128413707Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_2Reimported from Input_DNMT_WT_ES_222900860Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo
Input_DNMT_WT_ES_3Reimported from Input_DNMT_WT_ES_320708029Visible stores parser Filter by feature Excluding excluded_regions_all_input_200425.txt Remove DuplicatesNo

Replicate Sets

ATAC_DNMT_KO_EpiATAC_DNMT_KO_ESCTCF_DNMT_KO_EpiCTCF_DNMT_KO_ESCTCF_DNMT_WT_EpiCTCF_DNMT_WT_ESH3K27Ac_DNMT_KO_EpiH3K27Ac_DNMT_KO_ESH3K27Ac_DNMT_WT_EpiH3K27Ac_DNMT_WT_ESH3K27me3_DNMT_KO_EpiH3K27me3_DNMT_KO_ESH3K27me3_DNMT_WT_EpiH3K27me3_DNMT_WT_ESH3K4me1_DNMT_KO_EpiH3K4me1_DNMT_KO_ESH3K4me1_DNMT_WT_EpiH3K4me1_DNMT_WT_ESH3K4me3_DNMT_KO_EpiH3K4me3_DNMT_KO_ESH3K4me3_DNMT_WT_EpiH3K4me3_DNMT_WT_ESInput_DNMT_KO_EpiInput_DNMT_KO_ESInput_DNMT_WT_EpiInput_DNMT_WT_ES
ATAC_DNMT_KO_Epi_1ATAC_DNMT_KO_ES_1CTCF_DNMT_KO_Epi_1CTCF_DNMT_KO_ES_1CTCF_DNMT_WT_Epi_1CTCF_DNMT_WT_ES_1H3K27Ac_DNMT_KO_Epi_1H3K27Ac_DNMT_KO_ES_1H3K27Ac_DNMT_WT_Epi_1H3K27Ac_DNMT_WT_ES_1H3K27me3_DNMT_KO_Epi_1H3K27me3_DNMT_KO_ES_1H3K27me3_DNMT_WT_Epi_1H3K27me3_DNMT_WT_ES_1H3K4me1_DNMT_KO_Epi_1H3K4me1_DNMT_KO_ES_1H3K4me1_DNMT_WT_Epi_1H3K4me1_DNMT_WT_ES_1H3K4me3_DNMT_KO_Epi_1H3K4me3_DNMT_KO_ES_1H3K4me3_DNMT_WT_Epi_1H3K4me3_DNMT_WT_ES_1Input_DNMT_KO_Epi_1Input_DNMT_KO_ES_1Input_DNMT_WT_Epi_1Input_DNMT_WT_ES_1
ATAC_DNMT_KO_Epi_2ATAC_DNMT_KO_ES_2CTCF_DNMT_KO_Epi_2CTCF_DNMT_KO_ES_2CTCF_DNMT_WT_Epi_2CTCF_DNMT_WT_ES_2H3K27Ac_DNMT_KO_Epi_2H3K27Ac_DNMT_KO_ES_2H3K27Ac_DNMT_WT_Epi_2H3K27Ac_DNMT_WT_ES_2H3K27me3_DNMT_KO_Epi_2H3K27me3_DNMT_KO_ES_2H3K27me3_DNMT_WT_Epi_2H3K27me3_DNMT_WT_ES_2H3K4me1_DNMT_KO_Epi_2H3K4me1_DNMT_KO_ES_2H3K4me1_DNMT_WT_Epi_2H3K4me1_DNMT_WT_ES_2H3K4me3_DNMT_KO_Epi_2H3K4me3_DNMT_KO_ES_2H3K4me3_DNMT_WT_Epi_2H3K4me3_DNMT_WT_ES_2Input_DNMT_KO_Epi_2Input_DNMT_KO_ES_2Input_DNMT_WT_Epi_2Input_DNMT_WT_ES_2
ATAC_DNMT_KO_Epi_3ATAC_DNMT_KO_ES_3CTCF_DNMT_KO_Epi_3CTCF_DNMT_KO_ES_3CTCF_DNMT_WT_Epi_3CTCF_DNMT_WT_ES_3H3K27Ac_DNMT_KO_Epi_3H3K27Ac_DNMT_KO_ES_3H3K27Ac_DNMT_WT_Epi_3H3K27Ac_DNMT_WT_ES_3H3K27me3_DNMT_KO_Epi_3H3K27me3_DNMT_KO_ES_3H3K27me3_DNMT_WT_Epi_3H3K27me3_DNMT_WT_ES_3H3K4me1_DNMT_KO_Epi_3H3K4me1_DNMT_KO_ES_3H3K4me1_DNMT_WT_Epi_3H3K4me1_DNMT_WT_ES_3H3K4me3_DNMT_KO_Epi_3H3K4me3_DNMT_KO_ES_3H3K4me3_DNMT_WT_Epi_3H3K4me3_DNMT_WT_ES_3Input_DNMT_KO_Epi_3Input_DNMT_KO_ES_3Input_DNMT_WT_Epi_3Input_DNMT_WT_ES_3

Quantitation

NameParentProbesDescriptionComments
2 kb tiles1362779Running windows of size 2000 with step size 2000. Quantitated with Read Count Quantitation using All Reads correcting for total count per million reads log transformed

DNMT_KO_ES_1 has a bit of an enrichment problem.

Hm, that's coming out slightly odd. Maybe because there is overall not that much enrichment/ defined peaks.

Babraham Bioinformatics