I do a lot of RNA-seq analyses with data from Illumina. My pipeline is usually mapping with topHat2, quantification with subread's featureCount, and statistics in limma or edgeR.
Now at our institute we have an Ion S5 available and we want to try the Ion AmpliSeq Transcriptome Solution for transcriptomics. This is a targeted amplification of ~20k genes (so not a whole transciptome analysis).
Does anyone has experience with the analysis of this protocol? Can I use the same pipeline for data analysis, or are there some caveats I have to be aware of? Please share your experiences, thanks in advance!