StringTie's merge function

Question

[amy16]

Is the stringtie's merge used to merge the transcripts fronm biological replicates prior to differential expression analysis?

Answer 1

[Kevin Blighe]

It can be used for that if you want - yes.

I believe that it was designed for situations where you want to just create a consensus transcriptome reference GTF from multiple samples, whatever they may have been. Take a look at the release notes:

1/3/2016 - v1.2.0 release

• new feature: a "transcripts merge" usage mode of StringTie which is triggered by the new --merge option; with this option StringTie expects as input a list of GTF files and merges/assembles all these transcripts into a non-redundant set of transcripts. This performs a
  function similar to the CuffMerge script in the Cufflinks/Tuxedo suite -- please see the updated protocol in the manual.

• an improved "estimation only" usage mode (-e option); in this mode only, StringTie now assigns reads to partially covered reference
  transcripts as well, therefore relaxing the previous requirement that reference transcripts need to be covered end-to-end in order to be
  found as expressed.

• improvements in dealing with abnormally large bundles by filtering of likely spurious spliced alignments produced by some aligners (e.g. STAR); note that HISAT2, used with the --dta option, is now the recommended aligner to use for StringTie.

[source: https://ccb.jhu.edu/software/stringtie/]

[amy16]

This term of multiple samples is what I am not clear about. Does it mean the biological replicates or different genotypes ? In my case, I have biological replicates, different genotypes with different tretment to identify differential gene expression.

[Kevin Blighe]

It can be absolutely anything that you want. The logic of why you are merging/comparing the transcriptomes needs to make sense. StringTie is just providing functionality for you to use in whichever way(s) you please.

Technically, you could merge the replicates independently with each other, and then further perform a merge of all 'replicate transcriptomes'