SeqMonk Vistory

post-mapping QC H3K27me3

Project Summary

Basic Project Info

ParameterValue
Project Namepluripotency_exit_TET_K27ac_K27m_K4m_input.smk
Vistory Name[Not saved yet]
GenomeMus musculus GRCm38_v95
SeqMonk Version1.45.4

Data Sets

NameFile NameReadsImport Options
TET_KO_2i_H3K27me3_rep1_sensible_regionsReimported from TET_KO_2i_H3K27me3_rep151412598Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_H3K27me3_rep2_sensible_regionsReimported from TET_KO_2i_H3K27me3_rep228509635Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_H3K27me3_rep3_sensible_regionsReimported from TET_KO_2i_H3K27me3_rep363857991Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_H3K4me3_rep1_sensible_regionsReimported from TET_KO_2i_H3K4me3_rep125899278Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_H3K4me3_rep2_sensible_regionsReimported from TET_KO_2i_H3K4me3_rep250192846Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_H3K4me3_rep3_sensible_regionsReimported from TET_KO_2i_H3K4me3_rep342621203Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_HK27Ac_rep1_sensible_regionsReimported from TET_KO_2i_HK27Ac_rep128877898Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_HK27Ac_rep2_sensible_regionsReimported from TET_KO_2i_HK27Ac_rep221884813Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_HK27Ac_rep3_sensible_regionsReimported from TET_KO_2i_HK27Ac_rep334244229Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_Input_(from_K27Ac)_rep1_sensible_regionsReimported from TET_KO_2i_Input_(from_K27Ac)_rep121568372Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_Input_(from_K27Ac)_rep2_sensible_regionsReimported from TET_KO_2i_Input_(from_K27Ac)_rep225999091Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_2i_Input_(from_K27Ac)_rep3_sensible_regionsReimported from TET_KO_2i_Input_(from_K27Ac)_rep323911064Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K27me3_rep1_sensible_regionsReimported from TET_KO_EpiLC_H3K27me3_rep138162046Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K27me3_rep2_sensible_regionsReimported from TET_KO_EpiLC_H3K27me3_rep244042830Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K27me3_rep3_sensible_regionsReimported from TET_KO_EpiLC_H3K27me3_rep338915560Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K4me3_rep1_sensible_regionsReimported from TET_KO_EpiLC_H3K4me3_rep167260573Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K4me3_rep2_sensible_regionsReimported from TET_KO_EpiLC_H3K4me3_rep255942641Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_H3K4me3_rep3_sensible_regionsReimported from TET_KO_EpiLC_H3K4me3_rep349719423Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_HK27Ac_rep1_sensible_regionsReimported from TET_KO_EpiLC_HK27Ac_rep122760982Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_HK27Ac_rep2_sensible_regionsReimported from TET_KO_EpiLC_HK27Ac_rep240802061Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_HK27Ac_rep3_sensible_regionsReimported from TET_KO_EpiLC_HK27Ac_rep343247530Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_Input_(from_K27Ac)_rep1_sensible_regionsReimported from TET_KO_EpiLC_Input_(from_K27Ac)_rep128899190Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_Input_(from_K27Ac)_rep2_sensible_regionsReimported from TET_KO_EpiLC_Input_(from_K27Ac)_rep230319122Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_KO_EpiLC_Input_(from_K27Ac)_rep3_sensible_regionsReimported from TET_KO_EpiLC_Input_(from_K27Ac)_rep327791486Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K27me3_rep1_sensible_regionsReimported from TET_WT_2i_H3K27me3_rep131542293Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K27me3_rep2_sensible_regionsReimported from TET_WT_2i_H3K27me3_rep233319253Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K27me3_rep3_sensible_regionsReimported from TET_WT_2i_H3K27me3_rep336228135Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K4me3_rep1_sensible_regionsReimported from TET_WT_2i_H3K4me3_rep142525818Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K4me3_rep2_sensible_regionsReimported from TET_WT_2i_H3K4me3_rep262977267Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_H3K4me3_rep3_sensible_regionsReimported from TET_WT_2i_H3K4me3_rep349514618Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_HK27Ac_rep1_sensible_regionsReimported from TET_WT_2i_HK27Ac_rep150362930Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_HK27Ac_rep2_sensible_regionsReimported from TET_WT_2i_HK27Ac_rep278499168Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_HK27Ac_rep3_sensible_regionsReimported from TET_WT_2i_HK27Ac_rep333992477Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_Input_(from_K27Ac)_rep1_sensible_regionsReimported from TET_WT_2i_Input_(from_K27Ac)_rep136015833Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_Input_(from_K27Ac)_rep2_sensible_regionsReimported from TET_WT_2i_Input_(from_K27Ac)_rep232510519Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_2i_Input_(from_K27Ac)_rep3_sensible_regionsReimported from TET_WT_2i_Input_(from_K27Ac)_rep333866882Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K27me3_rep1_sensible_regionsReimported from TET_WT_EpiLC_H3K27me3_rep130086789Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K27me3_rep2_sensible_regionsReimported from TET_WT_EpiLC_H3K27me3_rep236051520Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K27me3_rep3_sensible_regionsReimported from TET_WT_EpiLC_H3K27me3_rep327897835Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K4me3_rep1_sensible_regionsReimported from TET_WT_EpiLC_H3K4me3_rep145962671Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K4me3_rep2_sensible_regionsReimported from TET_WT_EpiLC_H3K4me3_rep236222011Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_H3K4me3_rep3_sensible_regionsReimported from TET_WT_EpiLC_H3K4me3_rep330462670Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_HK27Ac_rep1_sensible_regionsReimported from TET_WT_EpiLC_HK27Ac_rep136423629Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_HK27Ac_rep2_sensible_regionsReimported from TET_WT_EpiLC_HK27Ac_rep231559786Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_HK27Ac_rep3_sensible_regionsReimported from TET_WT_EpiLC_HK27Ac_rep334532777Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_Input_(from_K27Ac)_rep1_sensible_regionsReimported from TET_WT_EpiLC_Input_(from_K27Ac)_rep135254403Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_Input_(from_K27Ac)_rep2_sensible_regionsReimported from TET_WT_EpiLC_Input_(from_K27Ac)_rep229614442Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo
TET_WT_EpiLC_Input_(from_K27Ac)_rep3_sensible_regionsReimported from TET_WT_EpiLC_Input_(from_K27Ac)_rep328771785Visible stores parser Filter by feature Excluding excluded_regions Remove DuplicatesNo

Replicate Sets

TET_KO_2i_H3K27me3TET_KO_2i_H3K4me3TET_KO_2i_HK27AcTET_KO_2i_Input_(from_K27Ac)TET_KO_EpiLC_H3K27me3TET_KO_EpiLC_H3K4me3TET_KO_EpiLC_HK27AcTET_KO_EpiLC_Input_(from_K27Ac)TET_WT_2i_H3K27me3TET_WT_2i_H3K4me3TET_WT_2i_HK27AcTET_WT_2i_Input_(from_K27Ac)TET_WT_EpiLC_H3K27me3TET_WT_EpiLC_H3K4me3TET_WT_EpiLC_HK27AcTET_WT_EpiLC_Input_(from_K27Ac)
TET_KO_2i_H3K27me3_rep1_sensible_regionsTET_KO_2i_H3K4me3_rep1_sensible_regionsTET_KO_2i_HK27Ac_rep1_sensible_regionsTET_KO_2i_Input_(from_K27Ac)_rep1_sensible_regionsTET_KO_EpiLC_H3K27me3_rep1_sensible_regionsTET_KO_EpiLC_H3K4me3_rep1_sensible_regionsTET_KO_EpiLC_HK27Ac_rep1_sensible_regionsTET_KO_EpiLC_Input_(from_K27Ac)_rep1_sensible_regionsTET_WT_2i_H3K27me3_rep1_sensible_regionsTET_WT_2i_H3K4me3_rep1_sensible_regionsTET_WT_2i_HK27Ac_rep1_sensible_regionsTET_WT_2i_Input_(from_K27Ac)_rep1_sensible_regionsTET_WT_EpiLC_H3K27me3_rep1_sensible_regionsTET_WT_EpiLC_H3K4me3_rep1_sensible_regionsTET_WT_EpiLC_HK27Ac_rep1_sensible_regionsTET_WT_EpiLC_Input_(from_K27Ac)_rep1_sensible_regions
TET_KO_2i_H3K27me3_rep2_sensible_regionsTET_KO_2i_H3K4me3_rep2_sensible_regionsTET_KO_2i_HK27Ac_rep2_sensible_regionsTET_KO_2i_Input_(from_K27Ac)_rep2_sensible_regionsTET_KO_EpiLC_H3K27me3_rep2_sensible_regionsTET_KO_EpiLC_H3K4me3_rep2_sensible_regionsTET_KO_EpiLC_HK27Ac_rep2_sensible_regionsTET_KO_EpiLC_Input_(from_K27Ac)_rep2_sensible_regionsTET_WT_2i_H3K27me3_rep2_sensible_regionsTET_WT_2i_H3K4me3_rep2_sensible_regionsTET_WT_2i_HK27Ac_rep2_sensible_regionsTET_WT_2i_Input_(from_K27Ac)_rep2_sensible_regionsTET_WT_EpiLC_H3K27me3_rep2_sensible_regionsTET_WT_EpiLC_H3K4me3_rep2_sensible_regionsTET_WT_EpiLC_HK27Ac_rep2_sensible_regionsTET_WT_EpiLC_Input_(from_K27Ac)_rep2_sensible_regions
TET_KO_2i_H3K27me3_rep3_sensible_regionsTET_KO_2i_H3K4me3_rep3_sensible_regionsTET_KO_2i_HK27Ac_rep3_sensible_regionsTET_KO_2i_Input_(from_K27Ac)_rep3_sensible_regionsTET_KO_EpiLC_H3K27me3_rep3_sensible_regionsTET_KO_EpiLC_H3K4me3_rep3_sensible_regionsTET_KO_EpiLC_HK27Ac_rep3_sensible_regionsTET_KO_EpiLC_Input_(from_K27Ac)_rep3_sensible_regionsTET_WT_2i_H3K27me3_rep3_sensible_regionsTET_WT_2i_H3K4me3_rep3_sensible_regionsTET_WT_2i_HK27Ac_rep3_sensible_regionsTET_WT_2i_Input_(from_K27Ac)_rep3_sensible_regionsTET_WT_EpiLC_H3K27me3_rep3_sensible_regionsTET_WT_EpiLC_H3K4me3_rep3_sensible_regionsTET_WT_EpiLC_HK27Ac_rep3_sensible_regionsTET_WT_EpiLC_Input_(from_K27Ac)_rep3_sensible_regions

Quantitation

NameParentProbesDescriptionComments
1kb tiles2725549Running windows of size 1000 with step size 1000. Quantitated with Read Count Quantitation using All Reads correcting for total count per million reads log transformed
Value above 0 in at least 11kb tiles318030[Probe Values Filter] Filter on probes in 1kb tiles where at least 1 of TET_KO_2i_HK27Ac , TET_KO_EpiLC_HK27Ac , TET_WT_2i_HK27Ac , TET_WT_EpiLC_HK27Ac had a value above 0.0. Quantitation was Read Count Quantitation using All Reads correcting for total count per million reads log transformed

Cumulative Distributions

PCA

New Probe List: Value above 0 in any (372469 probes)

[Probe Values Filter] Filter on probes in 1kb tiles where at least 1 of TET_KO_2i_H3K27me3 , TET_KO_EpiLC_H3K27me3 , TET_WT_2i_H3K27me3 , TET_WT_EpiLC_H3K27me3 had a value above 0.0. Quantitation was Read Count Quantitation using All Reads correcting for total count per million reads log transformed

TET_WT_2i_H3K27me3_rep2 is the funky one.

Looking at cumulative distributions only for these three replicates.

Hm, they look very similar.

DataStoreTotal Read CountForward Read CountReverse Read CountUnknown Read CountMean Read LengthTotal Read LengthFold CoverageTotal QuantitationMedian QuantitationMean QuantitationValid Quantitations
TET_WT_2i_H3K27me3_rep1_sensible_regions315422931577113115771162019561676059132.2628951282346046-5710051.130307021-1.8092905-2.09500962725549
TET_WT_2i_H3K27me3_rep2_sensible_regions333192531665565416663599018662295234502.285612677767764-5606899.79127475-1.7363561-2.05716352725549
TET_WT_2i_H3K27me3_rep3_sensible_regions362281351811489918113236019671011972372.6054298635342032-5632550.780120168-1.719607-2.06657482725549

Also similar read numbers

No issues with duplication ....

Hang on, it looks like TET_WT_2i_H3K27me3_rep3 is really a knock out.

1) Scatter is much more similar to the KO than to the other WT

2) Some of the genetic differences between WT and KO seem to be matching up with KO rather than WT

3) But most informatively, you can actually see the deletion of the exons in TET3. Tet1 and Tet2 don't have very many reads for K27me3 so while the 'hole' is there, it's a bit icky, but for Tet3 it's rather obvious.

I also checked all of the other samples and they are all the genotype they claim.

Babraham Bioinformatics