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Differential Expression analyses between species

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  • Differential Expression analyses between species

    Hi all,

    The project I am currently working on involves five closely related cricket species in the same genus. I have 8 (neutral) replicates of each species and the project was conceived with interspecific DE analyses in mind.

    So far, I have made 5 de novo transcriptomes (one for each species) and estimated transcript abundance with kallisto. I notice now that most of the software for making transcript and gene expression matrices (for example $TRINITY_HOME/util/abundance_estimates_to_matrix.pl) require a single reference file. This makes sense if you are comparing different treatment conditions or populations within a species, but how do you proceed when you have multiple reference files? If I were to use a single reference file for all species, surely that would introduce significant bias towards the species used as the reference?

    If anyone has any insight here, it would be greatly appreciated. In the mean time, I'll keep digging for answers.

    Thank you.
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