Is there a step-by-step tutorial on creating gene models for protists? (Maker?)

Question

[O.rka]

I have a diatom and I want to make gene models for this. I have the following files: (1) Repeat masked assembly; (2) RNA-seq reads; (3) RNA-seq bam files mapped to the assembly; (4) Protein homologs from other diatoms

I tried running funannotate but there are so many dependencies and the pipeline stopped at the prediction phase unfortunately. I've exhausted a lot of energy and time with funannotate.

I want to try maker but the tutorials are so verbose and it's extremely overwhelming. Is there any tool that is easy to run with well documented tutorial that is easily installed via conda?

Any well documented tutorials for Maker that makes it easy to run?

Answer 1

[lakhujanivijay]

Answer 2

[Juke34]

It’s pity to drop funannotate after having spent so much energy. There is no way to fix your problem? Maker has also lot of dependencies... if you have installed it give it a try. There are plenty of documentation less verbose made by users on internet.

If you are looking for other annoation tools I have a list here: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools.md