We have a question about the proper handing of ambiguous annotation reads when using DESeq2. In our bacterial RNAseq data there is a fraction of reads (0.5-2%) that map inconclusively to two adjacent genes (gene A and gene B). We count such reads twice, one for gene A and one for gene B. Can we use DESeq2 for such counting? We prefer not to exclude these reads because they may have biological meaning.
Thank you very much, Raya