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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Can I reuse the trinotate.sqlite database across multiple assemblies from different samples? #41

Closed davidecarlson closed 3 years ago

davidecarlson commented 3 years ago

Hi All,

I just finished running Trinotate for one transcriptome assembly, and I have possibly stupid question.

I plan to write a pipeline to run Trinotate to annotate 60+ transcriptome assemblies from different samples and get a report for each one. However, I don't have much experience with sqlite, and it's not clear to me whether I can reuse the same database for each assembly, or if I would need to rerun the Build_Trinotate_Boilerplate_SQLite_db.pl script each time.

Obviously, I would prefer to not have to rerun this script each time as it will just download databases that I already have available. Can I just load the results for each assembly and get a report for just that assembly, or is that not how this works?

Any insights? Thanks! Dave

brianjohnhaas commented 3 years ago

Hi Dave,

You need to have a separate sqlite database for each transcriptome.

When you run the initial boilerplate build process, just copy that boilerplate.sqlite file to a new filename that will be used for each separate transcriptome. You don't need to rerun the build process for each one.... just need to have the same basic boilerplate for each one to be populated separately.

best,

~b

On Mon, Jul 13, 2020 at 9:47 PM Dave Carlson notifications@github.com wrote:

Hi All,

I just finished running Trinotate for one transcriptome assembly, and I have possibly stupid question.

I plan to write a pipeline to run Trinotate to annotate 60+ transcriptome assemblies from different samples and get a report for each one. However, I don't have much experience with sqlite, and it's not clear to me whether I can reuse the same database for each assembly, or if I would need to rerun the Build_Trinotate_Boilerplate_SQLite_db.pl script each time.

Obviously, I would prefer to not have to rerun this script each time as it will just download databases that I already have available. Can I just load the results for each assembly and get a report for just that assembly, or is that not how this works?

Any insights? Thanks! Dave

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davidecarlson commented 3 years ago

Thanks, Brian!