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sleuth vs deseq2

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?

rna-seq deseq2 deseq
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updated by Kevin Blighe Kevin Blighe • written by Mozart Mozart

1 answer

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

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written by Kevin Blighe Kevin Blighe

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

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written by ivivek_ngs ivivek_ngs

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