I recently did RNASeq and have the Paired-end read, I have checked quality in FastQC and trimmed the ends with Trimmomatic. Does any one have a pipeline i could use to do downstream analysis. i have been learning online/youtube etc. No formal training on these kind of analysis. I am interested in differential expression profiles (compare Control and Treatment), and identify unique genes expressed at different stages on my treatment.
For an overview the different ways to analyze your data you can refere to this.
With regards to gene DE analysis there are two major ways you can go:
Option 2) I want to learn some bioinformatics and R coding along the way: Again there are many options but a good place to start is this workflow using DESeq2 which have links to the other things you need.