What are the steps to follow (or available methods), to compare and filter mutual transcripts from two different trancriptomes with high precision?

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The Optimal Experimental Approach for Gene Function Analysis?

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What is the acceptable p-value cutoff for GO enrichment analysis ?

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What happens in snapTotal- seq?

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Why my in vitro transcription doesn't work?

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Michal Okoniewski

Depends how you have those transcriptomes described... If those are already GTFs on the same genome: cuffdiff. If those are two RNA-seq experiments on different species - cross-map them and quantitate. If you need many-to-many blast on transcript sequences, likely you need a script, perhaps biopython would be good.

Chamara Janaka Bandara

Thanks Michal...!!!!! :)

Ankush Bansal

You may try Trinity Differential Expression.

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Differential-Expression

Thanks Ankush.... !!!!