I am new to RNA-seq data exploration. I would need to inspect and compare the RNA-seq coverage tracks for my gene of interest during Zebrafish development. The set of developmental stages are already present in ENSEMBL RNA-seq models for this species. I downloaded the corresponding bigwig files from ENSEML FTP site and loaded them in IGV.
My question is: are these tracks directly comparable in terms of peak heights? I guess that they are comparable only if read depth normalisation has already taken into account, but I could not find this information. The gene expression profile I visualise in IGV clearly does not match the gene expression trend I could find in GeneExpression Atlas database for the same experiment of origin (this is the dataset).
If the ENSEMBL tracks are not normalised, what would be the most straightforward way to create a sound visualisation of RNA-seq coverage tracks for my gene of interest along this set of developmental stages?
