what is the basic difference between genome guided transcript assemblyusing Trinity and stringTie/cufflinks

Question

[Bioinfonext]

I am not able to understand clearly what is the actually difference between genome guided assembly using Trinity and Cufflinks/StringTie?

I understand that both generates isoforms for particular locus?

then what is the actual difference?

Answer 1

[shunyip]

This provides a good explanation.

In layman's term, Cufflinks treats the genome as the truth and construct the transcriptome based on aligned reads. (ex. two reads may not be overlapping with each other, but the genome can provide the evidence of two reads being originated from the same transcript by showing that these two reads are right next to each other.)

On the other hand, Trinity simply uses the genome as a guideline to see approximately where the reads come from. Then, it will construct the transcriptome only based on the read sequences themselves. (ex. overlapping regions between reads)

So, Trinity requires a higher sequencing depth than Cufflinks/StringTie to work well.