Issue with StringTie Output File when using DESeq2 option

[jennaj]

The instructions are above, also here

@igor

A proper workflow is:

1. create gene models for every sample
2. merge individual gene models into a single “master” annotation using StringTie merge
3. and use the master annotation for read counting

The reads can be counted with StringTie or any other software, for example, featureCounts. For read counting with StringTie disable gene prediction.

Read counting should be done with the same annotation, for sake of comparison, hence, the two options were made incompatible.

More details can be found in this other Q&A

@gallardoalba

a detailed explanation of the necessary steps can be found in:

training.galaxyproject.org

Galaxy Training: De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis.

Cheers.