Various analysis we can do after the Denovo assembly of Transcriptome sequencing data

[sequencer.boy]

Dear All,

What all analysis we can do after the Denovo assembly of Transcriptome sequencing data of a species. I can mention some such as..

1. Do a Pathway analysis using KEGG.
2. Do a GO Annotation.
3. Try OrthoVenn to plot graphs for protein orthologs.
4. Try a BGI-WEGO plot.

This might be a broad question. But your inputs can help lot of researchers who are new to the Genomics and can give some ideas. Even a small input from you can be helpful.
Thank you.

Regards,
Sequencer Boy

[GenoMax]

For reference, cross-posted: https://www.biostars.org/p/169186/