Question About DMR Annotation Package

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5.7 years ago

kylin.qhl • 0

Hi,

I'm new to WGBS analysis. I have the human WGBS data from sequencing company along with a report. Now I'm trying to follow the report and replicating every step, but I got a problem with the DMR annotation. The company used Bismark to call the methylation sites and used DSS package in R to do DMR analysis. But I don't have an idea about which package they used to do the annotation and got the table below. enter image description here

This is the DMR result from the company:

enter image description here

Thanks very much for the further help!

R WGBS Annotation • 1.6k views

ADD COMMENT • link updated 5.7 years ago by h.mon 35k • written 5.7 years ago by kylin.qhl • 0

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Did you pay for the analysis? Demand this information, in details, from the company. How are you going to interpret or publish if you don't know the details?

ADD REPLY • link 5.7 years ago by h.mon 35k

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This data is from one of the collaborators' lab. They want me to do the analysis again instead of using the result from the company. You are right, I should write an email to the company for the information. I'm just curious about how to annotate the same sequence with different region and merge the two tables.

ADD REPLY • link 5.7 years ago by kylin.qhl • 0

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I'm just curious about how to annotate the same sequence with different region and merge the two tables.

I understand the "merge the two tables part", but not the "annotate the same sequence with different region". What do you mean?

ADD REPLY • link 5.7 years ago by h.mon 35k

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For example, chr1 29297:30663, the intro, promoter, exon etc can be identified separately and then for this single sequence there would be multiple rows in the final table. I'm not sure if this is clear? Thanks.

ADD REPLY • link 5.7 years ago by kylin.qhl • 0

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