Trinotate - Error in xls Annotation Report creation

Question

[oliver.tills]

Hi, I am running Trinotate-2.0.1 and have encountered an error in the xls file created.

If I filter by gene_ID in excel it becomes evident that data other than gene ID is in the gene ID column. It turns out that for 10 rows there is an error whereby data are offset, so that the SwissProt_BlastP column takes the place of gene ID and everything else is shuffled around.

My question is - is this a problem with the program, or have I inadvertently done something wrong? The error isn't fixed by deleting the annotation, excel or sqlite files and running again?

Here is a screenshot of the issue - https://www.dropbox.com/s/0dcp2kgvl3mmcb4/Screen%20Shot%202015-02-13%20at%2012.08.56.png?dl=0

Cheers,
Oli

[Ram]

Does trinonate actually export an xls file or a tsv/csv file? And are you using different systems in the process (exported in Mac, opened in PC or the other way around)?

[oliver.tills]

No apparently not!

Seems to be a tab delimited file, despite the xls extension. Thanks for asking the question about file formats, I should have twigged this.

[Ram]

So, maybe they're using a mix of vertical \v and regular \t tabs.

Answer 1

[pld]

The .xls files I have from trinotate open correctly, did you alter the file at all or change the delimiters in excel when you first opened it? All I can think of is if you said that fields are enclosed in backtick characters, which are used to delimit values within a field.

It should be tab-delimited with LF (\n) to delimit the ends of rows.

There are some bugs in Trinotate however, some of the entries under BLAST hits in results I've seen are truncated. Or there might be some extra characters in the names/symbols/descriptions of various hits.

It does look like some of the EOL characters are screwed up and all of the garbled rows involve Titin. Can you open the file in a text editor (like Notepad++) and display tab/EOL characters and show us the offending sections?