Add sleuth as DEseq2 alternative

[MarieLataretu]

sleuth

[MarieLataretu]

needs kallisto for quantification

[hoelzer]

@MarieLataretu ah interesting, thanks for checking this. But actually I also thought about including a quasi-mapping tool next to HISAT so we could also simply add kallisto as a new module and to produce input for sleuth.

But strange that no other input is possible? I thought sleuth might also simply work with a read count matrix produced by any tool?

[MarieLataretu]

Well, I'm not sure, if it would work with data from other tools out of the box.

When creating a sleuth object, the path (!) to the kallisto output for each sample is needed. The docu of sleuth says

To use sleuth, RNA-Seq data must first be quantified with kallisto, [...]

kallisto's output consists of abundance.h5, abundance.tsv and run_info.json

I think the best is to include kallisto in the pipeline.

[hoelzer]

Ok, thx. Then let's included a Kallisto Module. We can then calculate both

Kallisto-sleuth Hisat-deseq

And compare. I would be interested in how the "aln-free" performs.