Transcriptome assembly with variations among replicates

Question

[Cacau]

I have three biological replicates and want to assembly the transcriptome. How should I deal with the differences among replicates？ For example, how to deal with different transcription start sites?

[GenoMax]

It is the same sample and you want to get a comprehensive transcriptome representation, correct? Go with all three pooled together for assembly. You can individually align the samples to the transcriptome afterwards to judge differences (if any).

[Cacau]

Yes, that is what I meant. I would also like to see whether they are consistent. Thanks a lot.

Answer 1

[Cacau]

Any help? Or should I only use one replicate?