How to proceed after Trinotate?

Question

[Ismaelrymy]

Hi there.

I'm new to the field of transcriptomics, and, as such, finding information sometimes can be quite difficult. I have to assemble a reference transcriptome de novo, and i have made it through trimming, filtering, assembly, and almost annotation. I used Trinotate to annotate my first draft of the transcriptome, but now, I don't know how to proceed.

I have a .csv file, with all the blast results (and other annotations), but I don't know how to filter this information (one blast result has several transcripts, some of them complete, some fragmentary) and I would like to know how would you proceed in this step of the analysis.

If you have some kind of input or resources to check online I would be very grateful.

Answer 1

[Gio12]

You may consider predicting GO terms for your transcripts or evaluating the completeness of your transcriptome using BUSCO (https://busco.ezlab.org/). Additional details of your experiment (e.g. species of interest) may aid in getting better advice on this subject.