Addition:
For Artemis export to GFF, I changed "fasta_record" to "source", which
is a Feature Key in standard nomenclature*, and added the mandatory
fields /organism= and /mol_type=, but every time I get a message that
the source field cannot be exported.
Is that normal behaviour? Can anyone tell what goes wrong?
Cheers, Jack
* http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
On 10/21/2010 10:27 AM, j.vandevossenb...@science.ru.nl wrote:
Dear all,
I have annotated genome data in Artemis, and I would like to import the
result of that annotation into CLC Bio Genomics Workbench
(http://www.clcbio.com/).
I tried direct import, selected all entries and exported from Artemis to
EMBL, Genbank and Sequin. None of these were recognized by CLC, even
though it should be able to import many file formats
(http://www.clcbio.com/index.php?id=426).
I tried SFF, which does not include sequence data. So I used a separate
sequence file, the contigs concatenated into one large fasta sequence. CLC
has a SFF import filter, which is very picky about the sequence names
(read CLC SFF import manual). I managed to let it import SFF, but I did
not see any annotation at all, I think because all ORFs are named artemis
("gff_seqname artemis"). Contig names are lost in SFF, so this option may
import all annotated genes, but lose contig info. SFF does not recognize
"fasta record" so I should rename this into something (but what? I tried
"contig", "source", but the GFF file keeps on using ORFs only, all named
"gff_seqname artemis").
Does anyone have experience with this? I thought of using another program
as intermediate to convert Artemis data into CLC readable data.
Thanks for your help, Jack
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