de novo transcriptome annotation steps

Question

[confused_a_bit]

Hi all,

I am very new to bioinformatics and I have been reading many papers about annotation of a de novo transcriptome, but there are several ways and i am not sure which way to go about it. If you have any tips, I'd appreciate it

[Mark]

What organism are you working with?

[confused_a_bit]

a newly discovered species of triatomine bugs

[Mark]

Here's a really good protocol from a paper: https://www.protocols.io/view/de-novo-transcriptome-assembly-workflow-ghebt3e/abstract

One of the things I love is the detail and the multi-tool approach. I hope it helps!

Answer 1

[Juke34]

In my sense the hard part is the assembly not the annotation. As it is supposed to be mature RNA it is just matter to find the correct orf. I would go for transdecoder, and interproscan on the proteome you will get.