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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 Div I&I, Level 4 |
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