So basically I have RNA-seq reads that were generated from Illumina and Ion Torrent platforms for yeast species. I have seen an article where they compared liver cells of a rat that were sequenced with these two platforms, but they made use of PORT bioinformatics tool for the normalization of the data. This requires input data to be in the form of the Ensembl database. This database only has Saccharomyces cerevisiae annotation files available on it, whereas I have other species that I need annotation files for as well, which are available in RefSeq format from NCBI.
So, I am still brand new to doing RNA-expression analyses and have never done anything remotely at this scale. Please could anyone give me advice on the steps involved in analyzing the paired-end and single-end reads together as comparable data sets and then carrying out a complete differential expression analysis on this data. Any advice or guidance would really be appreciated, I am honestly not sure how to approach this at all.