Question: Is Kallisto Sleuth pipeline suitable for all organisms?
gravatar for SMILE
2.0 years ago by
SMILE120 wrote:

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?

rna-seq kallisto sleuth • 1.0k views
ADD COMMENTlink modified 21 months ago by prasundutta87360 • written 2.0 years ago by SMILE120
gravatar for aln
21 months ago by
aln290 wrote:

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.

ADD COMMENTlink written 21 months ago by aln290
gravatar for prasundutta87
21 months ago by
prasundutta87360 wrote:

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.

ADD COMMENTlink modified 21 months ago • written 21 months ago by prasundutta87360

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

ADD REPLYlink written 13 months ago by gabriel.jabud30
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