de novo transcriptome annotation steps
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
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Juke34
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confused_a_bit •
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confused_a_bit •
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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.
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What organism are you working with?
a newly discovered species of triatomine bugs
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!