Blueprint BS-Seq Dataset Inconsistency for Same Sample at Same Region

Question

[Shicheng Guo]

Here, the data is downloaded from , for the same sample and same region, you can find the significant inconsistency. very interesting, Hah. Any interpretation?

24821.Blueprint.ERS222212.WGB-Seq.signal.bigWig 0.722
24822.Blueprint.ERS222212.WGB-Seq.signal.bigWig 0.055
24829.Blueprint.ERS222236.WGB-Seq.signal.bigWig 0.789
24830.Blueprint.ERS222236.WGB-Seq.signal.bigWig 0.062
24813.Blueprint.ERS222206.WGB-Seq.signal.bigWig 0.007
24814.Blueprint.ERS222206.WGB-Seq.signal.bigWig 0.031
24811.Blueprint.ERS317235.WGB-Seq.signal.bigWig 0.318
24812.Blueprint.ERS317235.WGB-Seq.signal.bigWig 0.052
24835.Blueprint.ERS222243.WGB-Seq.signal.bigWig 0.393
24836.Blueprint.ERS222243.WGB-Seq.signal.bigWig 0.063
24839.Blueprint.ERS222245.WGB-Seq.signal.bigWig 0.264
24840.Blueprint.ERS222245.WGB-Seq.signal.bigWig 0.052
24809.Blueprint.ERS317234.WGB-Seq.signal.bigWig 0.761
24810.Blueprint.ERS317234.WGB-Seq.signal.bigWig 0.061
24893.Blueprint.ERS433785.WGB-Seq.signal.bigWig 0.915
24894.Blueprint.ERS433785.WGB-Seq.signal.bigWig 0.052
24895.Blueprint.ERS433789.WGB-Seq.signal.bigWig 0.935
24896.Blueprint.ERS433789.WGB-Seq.signal.bigWig 0.066
24903.Blueprint.ERS433793.WGB-Seq.signal.bigWig 0.904
24904.Blueprint.ERS433793.WGB-Seq.signal.bigWig 0.063

Okay. Interesting thing come out, I download the data from other blueprint website (hg38 reference):

ftp://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_progenitor_methylomes/meth/

And I found the values are usually <0.1, that means only one of the above value is right.

Roadmap: http://www.genboree.org/EdaccData/Current-Release/experiment-sample/Bisulfite-Seq/

DEEP don't provide batch download for his own data, they put the data into IHEC, now IHEC is charged by CA, see the following website and seems the data is terrible without uniform trimmed.

http://epigenomesportal.ca/ihec/download.html?session=8479