Hi, I am absolutely new to RNA-seq analysis. I would like to use this method to identify off-targets for my siRNA treatment. Basically i transfected or not transfected my cells in triplicate with that siRNA and then did RNA-seq in RNAs extracted from the samples for differential expression analysis (see how many genes were deferentially regulated). For the data generated, my colleague first aligned + mapped the library with STAR aligner, followed by the use of StringTie and Ballgown to study differential expression.
As an absolute rookie, my impression for RNA-seq is a heat map. However, in my case the transcriptome of treated cells is compared with those untreated, and that makes me think a one-lane heat map might look a bit odd. If I understand correctly, a better data presentation for my case may be: 1) a fold-change vs expression level (CPM) plot, or possibly, or 2) a volcano plot maybe. I am not sure if these types of plots can be drawn by Ballgown or any packages compatible with R (the only program available to me)? Can I used EdgeR or DEseq2 on data which have been processed by STAR and then StringTie?
Any help would be much appreciated! Lee