Comparing two different RNAseq datasets

Hi @Ubaid_Midhat!

The Deeptools suite might be what you are looking for to get information about the sequence depth/coverage variation between your samples. Please see: https://deeptools.readthedocs.io/

There is a domain-specific Galaxy server hosted through that web site, but you’ll also find these tools at public Galaxy servers. Examples: Galaxy EU https://usegalaxy.eu and Galaxy Main https://usegalaxy.org.

I’m not sure what your analysis goals are (expression? variation?) but the Galaxy tutorials might be helpful. Many tools have normalization functions/options. Please see: