TrinotateWeb confusion: Populating Trinotate.sqlite with Expression Data

[kurage]

Trinotate: samples_n_reads_described.txt

Dear Seqanswers group:
I am writing to get further clarification on an earlier post regarding the <<samples_n_reads_described.txt>> file to be used in Trinotate analyses.

>> Further, should the samples_n_reads_described.txt file just be manually made? That is, a modification of the provided sample, to suit my experiment?

What does "the provided sample" refer to?
Is there are template for how this file should be constructed?

Many thanks in advance.
Best,
Kurage

[TiborNagy]

For GO enrichment analysis I have used Bingo from Cytoscape.

[anth]

Yes.

Yes.

Thanks! It worked. I hope that Trinotate and TrinotateWeb continue to develop!

What have you done for downstream GO enrichment tests and pathway mapping, using Trinotate?

[TiborNagy]

...should the option "--DE_dir edgeR_trans/ \" simply be the absolute path to where all of my edgerR outputs are for the dataset?...

Yes.

Further, should the samples_n_reads_described.txt file just be manually made? That is, a modification of the provided sample, to suit my experiment?

Yes.

[anth]

I have run TrinotateWeb with the test data (and can view via the web interface and all), but I am confused by the usage with my own data.

Specifically, when I Populate Trinotate.sqlite with Transcript Expression Clusters, should the option "--DE_dir edgeR_trans/ \" simply be the absolute path to where all of my edgerR outputs are for the dataset?

Further, should the samples_n_reads_described.txt file just be manually made? That is, a modification of the provided sample, to suit my experiment?

Thank you,

Anthony