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  • Multi species RNA-seq comparison

    Hi all,

    I have count tables from two species. I'd like to find the find orthologous genes between the species and compare how the orthologs respond to a treatment using DESeq2. My question is:

    Should I create a dual-species count table containing only the orthologous genes and then run DESeq so all size factors can be estimated together OR should I do the differential expression on a species by species basis and merge the orthologous genes together once the log2foldChanges have been determined?

    I'd like to make bar graphs of the normalized counts for genes across species (which I couldn't do if I process each species separately), but am worried that removing genes without orthologs will mess with the negative binomial distribution needed for the size factor estimation

    Thanks for your help,

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