names for Trinotate

[jm...@ualberta.ca]

Hi,

I am trying to run a transcriptome published by another lab through Trinotate. The transcriptome was assembled with Trinity but they changed the transcript names. So I changed the names to:

>TR1|c1_g1_i1

>TR1|c1_g2_i1

>TR1|c1_g3_i1

etc.

But when trying to load transcripts into Trinity.sqlite, I received the error:
Error, no gene_id for trans: [TR1|c1_g1] 

This error seemed to be subverted by changing the transcript names to:

>TR1|c1_g1_i1

>TR2|c1_g2_i1

>TR3|c1_g3_i1

etc.

Loading the peptide sequences with these names, however, did not work  (these sequences were also provided by the other lab). I would guess I need to run the nucleotide sequences through TransDecoder which would also generate names in the correct format.

I'll have to rerun this transcriptome through TransDecoder, BLAST, and HMMER again. So before doing so I just wanted to confirm that if I changed all the names to the above should everything work? For continuity I still have to work with Trinity 2.0.6.

Thanks for your help!

Jasmine

-- 

MSc student, Leys Lab

Department of Biol. Sci.

University of Alberta

587.778.9683

[Brian Haas]

Hi Jasmine,

What's the command that you're running that's throwing the error?

best,

~brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas