using published genomic data

usegalaxy.eu support
1

Hi,

I would like to combine samples from different studies to do differential gene expression. For example, paper 1 has published 10 nasal samples from healthy children and 10 nasal samples from children with COVID infections; and paper 2 from a different research group has published 10 nasal samples with influenza infections. They may or may not have used the same sequencing platform/kits and seq depths.

Can I download the samples from both papers and do the the following DEG/pathway analyses etc on the dataset:

healthy children from paper 1 (as Factor 1), COVID from paper 1 (as factor 2)
healthy children from paper 1 (as Factor 1) and influenza from paper 2 (as Factor 2)?
COVID from paper 1 (as Factor 1) and influenza from paper 2 (as factor 2)
Healthy children (factor 1) vs COVID (factor 2) vs. Influenza (factor 3)

Since I will be using the same bioinformatic tools and commands to process both sets in the same analysis and all transcripts will be aligned to the same assembly, will this normalize data correctly and allow for valid comparisons?

Thanks,
Swati

2

Hi @seq2022
maybe ask people at a bioinformatics forum or DGE software developers. How do you distinguish between batch effect and potential biological effect in the described scenario with one condition coming from a different source?
Kind regards,
Igor