Hello there, just a quick talk about these different two approaches. I know that there is not a gold standard but I think it would be important for me to understand how these two approaches manages your data. Because they do it differently but I am not entirely sure that got it correctly. I mean I am not sure how sleuth manage transcript level counts in this sense.
It doesn't summarise transcript level counts, right?
Hi Mozart, still playing good music? - got any new compositions coming up for Christmas?
I've added deseq and deseq2 tags so that @MichaelLove may pick it up in addition to my answer.
Did you read the manuals for both of these programs?
Sleuth was designed to analyse Kallisto-generate data (see here), which can
include either transcript isoform level or gene-level counts.
DESeq2 can analyse raw counts from any source, again being either transcript isoform level or gene-level.
A package in R, tximport can be used to import raw counts into either Sleuth or DESeq2, and tximport can additionall summarise tanscript isoform counts to gene-level
I second that what Kevin is saying, however I would like to highlight the paper that should give you an idea of this as well since we performed this test as well. Take a look at rnaonthebench
I second that what Kevin is saying, however I would like to highlight the paper that should give you an idea of this as well since we performed this test as well. Take a look at rnaonthebench