Several gene annotations have been made on the fungal species I'm working on.
I would like to cross and validate those data to get just one annotation, which would be the closest to the reality.
For this task I have several RNAseq sets of data, obtained in different conditions.
With that, I would like to perform transcriptome assembly, to get transcripts predictions, and confront them to the annotations.
I was wondering if it is a better idea to do transcriptome assembly on each RNA-seq independantly, and then gather the transcripts predicted, or to merge all the reads of all RNA-seq in one file, and to perform the assembly on this file.
Does anyone have an opinion on this?