I prefer to use Kallisto-Sleuth pipeline to do differential gene expression analysis now.
But there is one thing I am not sure, is Kallisto Sleuth pipeline also work well for organisms which have incomplete annotation such as chicken, quail, sheep etc. Since Kallisto use transcriptome reference and kallisto-sleuth has the assumption that the organism has (in theory) nearly complete annotation. So for organisms with very incomplete annotation, is it better to use the pipeline using genome reference?
Can anyone explain to me the advantages and disadvantages of using Kallisto Sleuth pipeline for these organisms with incomplete annotation?
Do you have other better options for these organisms?