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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Annotations for Proteomics data? #21

Closed neiladhikari closed 5 years ago

neiladhikari commented 5 years ago

Is it possible to get annotations for proteomics data? I loaded and ran trinotate with my blastp output file but ended up with an empty results/report file with only the headers. I obviously don't have any gene_trans_map, --transcript_fasta or transdecoder_pep files. Following are the commands I used: Trinotate Trinotate.sqlite LOAD_swissprot_blastp blastp.outfmt6 Trinotate Trinotate.sqlite report > trinotate_annotation_report.xls

Thanks, Neil

brianjohnhaas commented 5 years ago

Hi Neil

It won't fully operate without transcriptome data. You can still generate useful search results though by following the guidelines.

Best

-via googleFi

On Tue, Jun 4, 2019, 4:12 PM neiladhikari notifications@github.com wrote:

Is it possible to get annotations for proteomics data? I loaded and ran trinotate with my blastp output file but ended up with an empty results/report file with only the headers. I obviously don't have any gene_trans_map, --transcript_fasta or transdecoder_pep files. Following are the commands I used: Trinotate Trinotate.sqlite LOAD_swissprot_blastp blastp.outfmt6 Trinotate Trinotate.sqlite report > trinotate_annotation_report.xls

Thanks, Neil

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neiladhikari commented 5 years ago

How far do I expect to get in terms of results? Would I get any annotations using just the blastp file I have? In other words, if I followed all the guidelines correctly, would the commands above have given me annotations or resulted in an empty file like I got?

brianjohnhaas commented 5 years ago

sorry, when I meant guides, I was referring to just running the different protein-level computes. Trinotate won't work for you wrt pulling together a summary data table. You'd have to do that yourself somehow (could require writing a little python or other code..., nothing major though).

best,

~b

On Wed, Jun 5, 2019 at 12:43 PM neiladhikari notifications@github.com wrote:

How far do I expect to get in terms of results? Would I get any annotations using just the blastp file I have? In other words, if I followed all the guidelines correctly, would the commands above have given me annotations or resulted in an empty file like I got?

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