RNAseq analysis with Ion AmpliSeq Transcriptome Solution data

Question

[Benn]

Hello,

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!

[Sharp]

Our lab has used this RNA Ampliseq panel. 1) For data analysis, you can directly get read counts(or we usually say gene expression) of genes by using CoverageAnalysis, an Ion Torrent Service Plugin. 2) Then you can do further analysis (DEGs,GSEA, network analysis) with the gene expression just as other sequencing data.

Hope these can help.