Lesley,
If you are working on a PC, then this sounds like it might be a memory problem.
You can try the workaround described in FAQ 4 here:
http://www.sanger.ac.uk/Software/Artemis/faqs.shtml#faqs
yours,
Julian Parkhill
Lesley Nicolson wrote:
Hi – I would really appreciate help with a problem importing files from
ensembl export view (http://www.ensembl.org/Homo_sapiens/exportview).
I’ve exported human chromosomal sequence (500Mb) from ensembl export
view, with gene, vega and genscan features, as a flat file (saved as
text file). In notepad this looks comparable to files that I can open in
artemis (apart from the XX blank lines – but it makes no difference
removing these): example:
ID 17 standard; DNA; HTG; 500000 BP.
XX
AC chromosome:NCBI36:17:10050467:10550466:1
XX
SV chromosome:NCBI36:17:10050467:10550466:1
XX
DT 21-JUN-2006
XX
DE Homo sapiens chromosome 17 NCBI36 partial sequence 10050467..10550466
DE annotated by Ensembl
XX
KW .
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia;
On opening the file in artemis, the file is accessed (since I get a base
count and reports of trans splicing features) but the sequence does not
appear on the artemis screen. I can successfully import sequence into
Artemis if I export it as fasta from export view but this means I lose
annotation. I have tried saving the feature component of the original
file as *.tab file and reading this in once the fasta sequence is loaded
but this does not import features into the sequence (annotations are at
least partially accessed as I get trans splicing messages but no
sequence annotations appear in the sequence screen of artemis). I have
also tried importing into vectorNTI and exporting as embl file
(whereupon the sequence is accessed but I get a final error message
regarding ‘vntifkey not being suitable identifier for source’ and no
sequence appears in Artemis (I also get the message vntifkey on readable
files prior to sequence appearing in Artemis screen so I don’t think
this is related to the loading problem)).
I have tried a sequence a colleague can import into artemis (with
success) and he has tried my sequence (and similarly failed) so it does
not seem to be a problem peculiar to my installation of artemis/PC
environment.
Does anyone have any tricks/workaround/tips I might try ? Many thanks.
Regards,
Lesley Nicolson
Glasgow Veterinary School
Div I&I, Level 4 Sir Henry Wellcome Building
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--
Julian Parkhill
Head of the Pathogen Sequencing Unit,
The Sanger Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SA, UK
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