Question: McGill Epigenomics Mapping Centre BS-Seq Data Problem
2
gravatar for Shicheng Guo
7 months ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

Hi All,

I tried to download some BS-Seq data from McGill Epigenomics Mapping Centre ([Here Database Link][1])

I have a little assumption about the BS-Seq wig/bigwig files in http://epigenomesportal.ca/edcc/ database.

KNIH wig file is 0-10 scale, DEEP/CEEHRC wig files are 0-100 scale while blueprint and Roadmap are 0-1 scale. Anyone met this problem before?

It looks these wig file are coverage not methylation signal. the scale actually represent the sequence depth.

Thanks.

bs-seq mcgill scale • 232 views
ADD COMMENTlink modified 6 months ago by logicalhorus0 • written 7 months ago by Shicheng Guo7.4k

I wanted to use transcriptome and epigenome data from IHEC and also ran into the problem of different data formats depending on the publishing group, where it's often not even stated what the values in specific columns are supposed to represent.

Where can I obtain the raw data?

ADD REPLYlink written 6 months ago by logicalhorus0
2
gravatar for Shicheng Guo
7 months ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

I obtained a response from IHEC and it seems my assumption is right, each dataset is uploaded by different group.

The annotation tracks deposited on the IHEC Data Portal have been generated by each respective data producing consortia, each with their own softwares and parameters. This explains the difference you see across tracks of different groups. IHEC is currently working on generating a pan-IHEC dataset using a unified data analysis pipeline and standardized quality control metrics. It will however take several more months before we reach this step. If you want to do real comparison across IHEC members datasets, I would currently recommend obtaining the raw data.

ADD COMMENTlink written 7 months ago by Shicheng Guo7.4k
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