Trinotate

[Ruhi]

Hi

I am using trinotateWeb for a de novo transcriptome annotation

to import the FPKM and DE analysis I want to do use

TRINOTATE_HOME/util/transcript_expression/import_expression_and_DE_results.pl
--sqlite Trinotate.sqlite
--samples_file samples_n_reads_described.txt
--count_matrix Trinity_trans.counts.matrix
--fpkm_matrix normalized.FPKM
--DE_dir edgeR.Isoform.dir
--transcript_mode

when I run this command I get the following error

DBD::SQLite::db prepare failed: no such table: Samples(1) at dbdimp.c line 271 at /trinotate/2013-11-10/util/transcript_expression/../../PerlLib/Sqlite_connect.pm line 75.
Cannot prepare statement: no such table: Samples(1) at dbdimp.c line 271
Failed query: <select sample_id, sample_name from Samples> values:
Errors: no such table: Samples(1) at dbdimp.c line 271

Any thoughts or suggestions....

[GenoMax]

Error is referring to a missing table from the database. Did you get the database and loaded the data as indicated in step 1 here: http://trinotate.sourceforge.net/#LoadingSQLite Were there any errors?

[Ruhi]

Trinotate

Thanks for your response that did fix the error.