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?
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: