Does SQLite need any refresh?

[Farbod Emami]

Dear all, Hi.

I have used Trinotate for my annotation as is guided in Trinity and trinotate web-site:

Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta trinity_out_dir/Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder_dir/longest_orfs.pep

and now I want to run another projects with another blastx & p results and long-ORF inputs. Can I just input the new file in SQLite or I must refresh or clean the database for each new inputs (if yes, how)?

Thank you in advance

Farbod

[Brian Haas]

Hi Farbod,

You'd need to start from a fresh boilerplate database. You shouldn't try to reuse an earlier-populated database from another run.

best,

~brian

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[Farbod Emami]

Dear Brian, Thank you for your help. So, would you please tell me that which steps I must repeat again before loading new blast and longest-ORF files ?

1- 

curl -L https://github.com/Trinotate/Trinotate/archive/v2.0.2.tar.gz > trinotate.tar.gz

2- 

sudo apt-get install sqlite3

3-

wget "ftp://ftp.broadinstitute.org/pub/Trinity/Trinotate_v2.0_RESOURCES/Trinotate.sprot_uniref90.20150131.boilerplate.sqlite.gz" -O Trinotate.sqlite.gz

gunzip Trinotate.sqlite.gz

Appreciate all your efforts

Farbod

On Tuesday, May 26, 2015 at 3:09:33 PM UTC+4:30, Brian Haas wrote:

Hi Farbod,

You'd need to start from a fresh boilerplate database. You shouldn't try to reuse an earlier-populated database from another run.

best,

~brian

On Tue, May 26, 2015 at 12:32 AM, Farbod Emami <farbo...@gmail.com> wrote:

Dear all, Hi.

I have used Trinotate for my annotation as is guided in Trinity and trinotate web-site:

Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta trinity_out_dir/Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder_dir/longest_orfs.pep

and now I want to run another projects with another blastx & p results and long-ORF inputs. Can I just input the new file in SQLite or I must refresh or clean the database for each new inputs (if yes, how)?

Thank you in advance

Farbod

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[Brian Haas]

Hi Farbod,

You don't need to reinstall any software. You just need to start with a fresh boilerplate sqlite database (your step 3) and load it with your new results.

~b

[Guandong Yang]

Hi Brian:

Can you be more specific on how to refresh the sqlite database for another annotation?

Guandong Yang

在 2015年5月26日星期二 UTC+8下午7:05:28，Brian Haas写道：

[Brian Haas]

Sure thing.

You download a new boilerplate sqlite database and populate it with your new data. 

best,

~brian

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[Brian Haas]

Excellent!  Thanks for the update!

~b

On Tue, Nov 3, 2015 at 4:07 AM, 杨冠东 <yanggua...@gmail.com> wrote:

Thank you! I have got the all the gene annotated!

Best Wishes

Guandong Yang

2015-10-31 2:51 GMT+08:00 Brian Haas <bh...@broadinstitute.org>:

Here you go:

 https://github.com/trinityrnaseq/trinityrnaseq/wiki/Functional-Annotation-of-Transcripts

This is basically what I do.

best,

~brian