Comparing two different RNAseq datasets

[Ubaid_Midhat]

Hi,
I was wondering if there is a way to compare two RNAseq datasets that were obtained for the same species, tissue and development stage but were from different batches, different runs, and also differ in read length and depth. I understand that the variation from such datasets would be fairly high but is there anyway to normalize these datasets e.g. using set of house keeping genes etc. to compare the datasets? If so, how can I normalize the datasets?
Thank you,
Midhat

[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.