As part of a presentation on bias modeling for RNA-seq, I put together a Shiny app that allows one to explore the differences between Salmon and kallisto on all samples from GEUVADIS and SEQC. For all datasets, we see that Salmon has more consistent estimation across labs, as described in the Salmon paper. You can click on the overview plots to explore the estimated counts by different methods for individual genes, where often the inconsistencies are driven by mis-estimation of which isoform is expressed within a gene.
- The Salmon kallisto diffs GitHub repository where you can find the Shiny app comparing Salmon and kallisto abundance estimates on these benchmarking datasets.
Example images (link to presentation slides):
Image may be NSFW.
Clik here to view.
