Is Kallisto Sleuth pipeline suitable for all organisms?

Question

[SMILE]

Hi all,

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?

Answer 1

[aln]

I'm analyzing some sheep data now, so I was also wondering if Kallisto-Sleuth has a significant disadvantage in this case. I plan to try several other pipelines and check if the results are extremely different.

Answer 2

[prasundutta87]

Since Kallisto aligns reads to a reference transcriptome, rather than a reference genome, technically, the transcriptome needs to be the best..but again, a transcriptome is good when the reference genome is good..if the N50 of the genome is decent and there are not many unplaced scaffolds (in thousands), you are good to go..OR, assemble your own transcriptome using transcriptome assembly tools such as Trinity, as you already have RNA-seq reads.

[gabriel.jabud]

How would you then add annotations to the Kallisto file following a Trinity de-novo assembly?