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Transcriptome assembly with variations among replicates

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?

rna-seq rna-seq assembly
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written by Cacau Cacau

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).

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written by GenoMax GenoMax

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

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written by Cacau Cacau

1 answer

Any help? Or should I only use one replicate?

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written by Cacau Cacau

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