Re: [Artemis-users] Export annotated Artemis data to CLC Bio
Hi Jack
Artemis is not really meant as a conversion tool between formats and in
particular EMBL/GenBank to GFF, although it will have a go. You could try
EMBOSS (seqret) to convert. However, it sounds like you have multiple fasta
records in your file which may cause problems if you are writing out embl
files. So you may want to try writing the sequence out (File->Write->All
bases). Open this single sequence file and then read your annotation into
the sequence entry. Then write out the file as EMBL.
Regards
Tim
On 10/21/10 12:26 PM, "Jack van de Vossenberg"
wrote:
> 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
>>
>>
>> ___
>> Artemis-users mailing list
>> Artemis-users@sanger.ac.uk
>> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>>
>
>
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Re: [Artemis-users] Export annotated Artemis data to CLC Bio
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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Artemis-users@sanger.ac.uk
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[Artemis-users] Export annotated Artemis data to CLC Bio
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_seqnameartemis").
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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