Good morning, I've just got the results of an Illumina Ampliseq RNA Targeted experiment, which consisted of analyzing differences in expressions among 250 genes. My data will probably consists of reads and won't be in the form of already 'quantified' reads. ..............
Is there any tool in Bioconductor which may help me with RNA Targeted data? Is it possible to simply align the results to a reference genome, or instead to the list of RNA Targeted genes? But, above all, which approach should perform better in this case to compare expression levels downstream and perform DE analysis? edgeR, DESEQ2 or limma? I've read the former two assume most genes are not differentially expressed, and apparently limma is more suited for microarrays. What do you think? Any experience here?
Thanks in advance!
