Transcriptome mapping without reference.

Question

[tiagobellintani]

Hello friends.

I would like to list a discussion on transcriptome mappings.

In the case of assembly without reference, the ideal would be to map as reads itself, however, nearby species can be useful in this mapping, how could genomes from nearby biological genera be used?

[Dunois]

If you can get protein sets for related taxa, you could search your own assembly's translated sequences against those to look for homologs. So not quite the genome itself, but something derived from it.

I suppose mapping the reads against a well-annotated genome of a closely related species could be used as a proxy for investigating gene expression patterns in presumptive orthologs?

[tiagobellintani]

Thanks, Dunois

Answer 1

[GenoMax]

Since you are going to have reads from your experiment just assemble a transcriptome using those. You could use related species to check for completeness of your assembly.