Question: Meta-analysis of two datasets.
gravatar for parveenkayenat
6 weeks ago by
parveenkayenat0 wrote:

Hello, I would like to perform meta-analysis on two datasets but both the datasets has different genome assembly, that is, one dataset has genome build 37 and another dataset has genome build 38. How do i perform meta-analysis? Is there any other software to perform meta analysis on different assemblies. Additionally, i have to perform Meta-analysis on quantiative traits, my study is not based on case-control association.

Please help me in this regard. Thank you in advance.

snp assembly gene • 139 views
ADD COMMENTlink written 6 weeks ago by parveenkayenat0

What is the data and what do you want to find out from it?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by rpolicastro3.9k

The data is the result of GWAS of quatitative traits. I want to perform meta-analysis on those two datasets and see the reaction of genes in statistical way. Without performing lifover, is it possible to run meta-analysis on two different assemblies datasets? Thank you in advance

ADD REPLYlink written 6 weeks ago by parveenkayenat0

liftOver might be relevant, see:

ADD REPLYlink written 6 weeks ago by zx87549.9k

I am using NCBI remapping for liftover. But when i put "1:752566:A:G" as an input, it shows that error in format and when i put "1:752566" then it works. So, if it work without the allele information then how do i correlate b37 assembly to b38? Is the allele information is same in build 37 and build 38? Thank you in advance.

ADD REPLYlink written 6 weeks ago by parveenkayenat0


You can try CrossMap for genome coordinates conversion between different assemblies.


ADD REPLYlink written 6 weeks ago by DM20
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