User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl510
Reputation:
510
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
20 hours ago
Joined:
1 year, 9 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Invertebrate phylogenetic tree on Ensembl
... Hi, Invertebrate species are represented by the Ensembl Genomes project: http://ensemblgenomes.org The Ensembl genomes project is split into five divisions: plants, protists, fungi, non-vertebrate metazoans and bacteria. Ensembl Genomes produces phylogenetic trees for each taxa division, e.g: ht ...
written 9 days ago by Ben_Ensembl510
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Answer: A: How to retrieve Ensembl phenotype data associated with Ensembl variations using
... Hi Chilam, The script works when I run it on my machine with my own sample data. I used a test file with variants: rs991426868 0 phenotype records rs699 5 phenotype records rs2238612 1 phenotype record I suggest that the variant name is also output ($var->name), as a check fo ...
written 5 weeks ago by Ben_Ensembl510
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Comment: C: Reference and mutant allele of a SNP rsID
... Hi Deepak, I think you'd be most interested in the "allele_string" listed as C/T for this variant, for example: http://rest.ensembl.org/variation/human/rs56116432?content-type=application/json This is the reference allele / alternate allele. i.e C is the reference allele, T is the alternate allele ...
written 7 weeks ago by Ben_Ensembl510
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Answer: A: Reference and mutant allele of a SNP rsID
... Hi Deepak, This is something that you can do with the Ensembl REST API with the following POST request: http://rest.ensembl.org/documentation/info/variation_id Best wishes Ben Ensembl Helpdesk ...
written 7 weeks ago by Ben_Ensembl510
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Answer: A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
... Hi JMallory, The BiomaRt query you have used here will retrieve all genes linked specifically with that GO term. The amiGO2 browser is returning all genes associated with that GO term AND its daughter terms. You can retrieve the list of genes associated with the GO term AND its daughter terms in ...
written 7 weeks ago by Ben_Ensembl510
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Answer: C: Ensembl ID converter not working?
... Having looked into this problem- it's caused by the way that retired Ensembl stale IDs are labelled in our database. This means that the ID history convertor does not recognise retired stable IDs and simply lists the retired stable ID for the current Ensembl release. This is only a problem where an ...
written 8 weeks ago by Ben_Ensembl510
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Comment: C: Ensembl ID converter not working?
... Hi, This is strange behaviour- and I think you may have found a bug in the ID history convertor. I think the problem arises from where we updated form the Galgal4 assembly to the Gallus_gallus-5.0 assembly. For example, searching in the Ensembl archives (in a version that used the Galgal4 assembl ...
written 9 weeks ago by Ben_Ensembl510
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Comment: C: How to edit a google drive URL for upload to ensembl browser?
... Hi Xavi, No problem- very happy to help. Please do let me know how you get on and if you have any other questions. Best wishes Ben Ensembl Helpdesk ...
written 3 months ago by Ben_Ensembl510
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Answer: A: How to edit a google drive URL for upload to ensembl browser?
... Hi Xavi, It is not possible to upload custom data to Ensembl via Google Drive. We would advise contacting your IT department, as they are likely to have a public directory (for example FTP) that you can use to store this data and link to Ensembl by providing the URL describing the location and name ...
written 3 months ago by Ben_Ensembl510
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Comment: C: biomaRt getSequence() connection time-out
... Hi Flaviu, I'm sorry to hear that you're still experiencing problems, but glad to see you've managed to find a work around. We'l carry on looking into this. Best wishes Ben ...
written 5 months ago by Ben_Ensembl510

Latest awards to Ben_Ensembl

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 5 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 7 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Supporter 11 weeks ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 12 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 15 months ago, created a post with more than 5 votes. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016

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