Comparing two different RNAseq datasets

[jennaj]

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:

@jennaj

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.