Question: Meta-analysis of two datasets.
0
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

Hi,

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

CrossMap

ADD REPLYlink written 6 weeks ago by DM20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2734 users visited in the last hour
_