Differential gene expression analysis after transcriptome assembly with SPAdes

Question

[langziv]

Hello.
I'm was recommended to use SPAdes for transcriptome assembly. I didn't find explanation on quantification and differential expression analysis after the assembly in the program's documentation, Does anybody have any recommendations for proper programs?

[GenoMax]

Once you have an assembled transcriptome use salmon or kallisto as you normally would.

Answer 1

[Istvan Albert]

As GenoMax points out follow any protocol that operates on the same type of information (in this case transcriptome data).

At the same time do account for the potential of using a more noisy and less accurate representation. Basically spend more time on validating the various counts and alignments/classifications.