Trinotate

[berger juliette]

Hello Brian, 

I am annotating my transcriptome with Trinotate, when I try to get the report.xls file, I don't get the full file load. I can't use singularity because of the difficulty of installing a lot of software, so I load my annotation file with cmd as follows:

"/home/bergerju/TRINOTATE/Trinotate-Trinotate-v4.0.0/Trinotate -db /home/bergerju/TRINOTATE/Crypto_Trinotate.sqlite \

        --LOAD_swissprot_blastx /home/bergerju/Cryptocercus/Seq_Trimme/blastx.outfmt6 \".

This is my report file :

 #gene_id        transcript_id   sprot_Top_BLASTX_hit    infernal        prot_id prot_coords     sprot_Top_BLASTP_hit    Pfam    SignalP TmHMM   eggnog  Kegg    gene_ontology_BLASTX           gene_ontology_BLASTP    gene_ontology_Pfam      transcript      peptide

TRINITY_DN218510_c0_g1  TRINITY_DN218510_c0_g1_i1       .       .       .       .       .       .       .       .       .       .       .       .       .       .       .
TRINITY_DN218556_c0_g1  TRINITY_DN218556_c0_g1_i1       .       .       .       .       .       .       .       .       .       .       .       .       .       .       .
TRINITY_DN218528_c0_g1  TRINITY_DN218528_c0_g1_i1       .       .       .       .       .       .       .       .       .       .       .       .       .       .       .
TRINITY_DN218481_c0_g1  TRINITY_DN218481_c0_g1_i1       .       .       .       .       .       .       .       .       .       .       .       .       .       .       .
TRINITY_DN218565_c0_g1  TRINITY_DN218565_c0_g1_i1       .       .       TRINITY_DN218565_c0_g1_i1.p1    2-301[-]        .       .       .       .       .       .       .       .              .       .       .

Do you have an idea where does it come from ?

Best Regards, 

Juliette

[Brian Haas]

Hi Juliette,

Does your file:  /home/bergerju/Cryptocercus/Seq_Trimme/blastx.outfmt6 have Trinity transcript or Trinotate protein ids in it?

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Brian J. Haas
The Broad Institute
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[Brian Haas]

Hi Juliette,

It looks like you might not have searched the swissprot database that Trinotate provides to you in the TRINOTATE_DATA_DIR/ after running the initial --create command.  The identifiers in that sprot fasta file are needed to match what's in the boilerplate sqlite database.

Try redoing the blast (using diamond, it's super fast), and then loading again.

best,

~b

On Tue, May 16, 2023 at 2:25 PM berger juliette <bergerju...@gmail.com> wrote:

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