Re: How to convert gb to gbk to get proper input for mauvealigner?
Hi Andreas and Afif,
>> a colleague of mine relaised that mauvealigner seems to need gbk files
>> when running under Linux (while under Win also gb file is working). This
>> happens when using
>>
>> java -Xmx6g -cp /usr/share/java/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output OUTPUTDIR -ref REFERENCE.gbk -draft DRAFT.contigs.fasta
>>
>> While under win also REFERENCE.gb is OK this leads to an error under
>> (the Debian packaged!) mauvealigner (I forgot to ask what version is
>> used under Win - may be there is a difference as well).
>
> As far as I know, gb and gbk are interchangeable extensions for the
> genbank format.
I am not aware of a systematic difference betweek 'gb' and 'gbk' files
either.
> The genbank format may or may not include the actual
> sequence data. If you're passing a genbank file to Mauve, it should be
> including the sequence data.
This is also the most obvious source of problems I could think of. If
one of the files only has the annotation (feature table) and no
sequence, this might result in an error.
What is the exact wording of the error message?
Cheers
Sascha
P.S. To order contigs along a reference one might also try ABACAS, which
only needs a FASTA sequence as the reference if I am not mistaken.
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