Problem with Trinotate boilerplate sqlite database

[Lucila Traverso]

Hi all,

I am trying to run Trinotate and I would really appreciate your help.

I have problems with the step of building the sqlite database. I am following the instructions in https://trinotate.github.io/, and it says that I have to generate it with TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl, nevertheless this script is not in the admin folder where I have it installed. My Trinotate version is Trinotate-2.0.2. I it would be very useful to me if I can use that version because that is the one I have available at the moment.

I have read that there is one database available online at

https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz

but I understand it is for version 3 of Trinotate.

So, can I use it anyway? Or do I have a script in v2 with a different name that I can use?

Thank you so much for your help.

Lucila

[Brian Haas]

Hi Lucila,

The data resources we used with Trinotate v2 are here:

https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v2.0_RESOURCES/

but they're pretty old at this point, and it would be best to upgrade sooner than later.

Also, I can only provide tech support for the latest version.

best,

~b

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

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

 

[Lucila Traverso]

Hi Brian,

thank you so much for your fast response. I will try to get it updated where I am working.

Best,

Lucila.

[Lucila Traverso]

Hello again Brian, I ran it and it worked. But I noticed that the top BLAST hits do not contain the full header of the sequence. For example, in the results table, I obtain "sp|Q10126|YSM6_CAEEL^sp|Q10126|YSM6_CAEEL^Q:62-352" instead of ">sp|Q10126|YSM6_CAEEL Putative uncharacterized transposon-derived protein F52C9.6 OS=Caenorhabditis elegans OX=6239 GN=F52C9.6 PE=5 SV=1".

So the question is: Do I have to perform the blast with some flag to capture all the header in the result, or this should work with the blast script suggested in the Trinotate pipeline?

Thank yo so much,
Lucila.

[Brian Haas]

When you search the Swissprot file that’s generated by trinotate as part of the initial build process, I expect it’ll contain the product name in the report.  When a custom database is searched, I think only the accession is provided instead of the defline.  This is because only swissprot data is structured and stored in the trinotate SQLite database 

-Brian

(by iPhone)

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.