I wist to use tximport followed by DeSeq2 for differential expression analysis of RNA-Seq data quantified by Salmon (from fastq files). The libraries are 3' end biased and have limited isoform level information (situation similar to that shown in Figure 1C of the Sonenson et al paper on the tximport package). I am trying to find the best set of parameters for DE analysis. Is it better to use the transcript length offset for normalization in this case?
Monell Chemical Senses Center