search

hputnam / Meth_Compare

5 stars 2 forks source link

Create bed files of MBD v WGBS and RRBS DMC for genome feature annotation #63

Closed mgavery closed 4 years ago

mgavery commented 4 years ago

@yaaminiv , passing you these bed files for the 50% DMC between MBDvWGBS: https://github.com/hputnam/Meth_Compare/blob/master/analyses/Pact_methDiff/Pact_WvM_50pMethDiff.bed MBDvRRBS:https://github.com/hputnam/Meth_Compare/blob/master/analyses/Pact_methDiff/Pact_RvM_50pMethDiff.bed

for annotation of genome feature from your pipeline.

mgavery commented 4 years ago

Just throwing this out there that the 50% cutoff is pretty random. See histograms of diff meth for WGBS v MBD for example: https://github.com/hputnam/Meth_Compare/blob/master/analyses/Pact_methDiff/MethCompare_DiffMethHisto_Pact_WvM_TG_050420.jpg

yaaminiv commented 4 years ago

Not sure how you wanted them visualized, but for now I generated count summary tables in this script from data I generated in this pipeline:

yaaminiv commented 4 years ago

Will do statistical comparison for all vs. method-associated DMC information

yaaminiv commented 4 years ago

DMC chi-sq test output here: https://github.com/hputnam/Meth_Compare/blob/be25687cdb0d1e47472680cd3da27430b5a589cd/analyses/Identifying-genomic-locations/Pact/Pact-DMC-Genomic-Location-StatResults.txt

hputnam commented 4 years ago

changing statistical approach for this.