User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl220
Reputation:
220
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
2 days, 11 hours ago
Joined:
1 year, 1 month ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Figure quality browser tracks
... Hi, As an alternative suggestion, this is something that you can do with the Ensembl browser. For the bigwig files, you can upload your own files to view in Ensembl: http://www.ensembl.org/info/website/tutorials/userdata.html For the conservation data, you can add tracks, for example, that show G ...
written 5 days ago by Ben_Ensembl220
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Answer: A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
... Hi there, Ensembl uses Sequence Ontology (SO) terms tho describe the consequences of variants. The upstream/ downstream consequence type is defined as being within 5kb of the transfer: http://www.sequenceontology.org/browser/current_svn/term/SO:0001631 So, a particular variant could be an upstream ...
written 6 days ago by Ben_Ensembl220
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Answer: A: Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Se
... Hello, Yes, these files look right for the analysis you wish to perform. With regards to the GTF, the README should clear this up for you: ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens//README .gtf: this is the default file, it should contain the full annotation for all species except huma ...
written 8 weeks ago by Ben_Ensembl220
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Answer: A: Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Se
... Hello, As I work within the Ensembl team, I'll answer our question from an Ensembl point of view. You may want to get advice form others regarding how you can link the information together between the different resources. Although we don't have web-based tool available for you to do this sort anal ...
written 8 weeks ago by Ben_Ensembl220
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Comment: C: How to retrieve COSMIC variations using Ensembl REST API?
... The 'variant_set' filter only works with the 'variation' feature type. We will change the text to clarify this for e!88, though. ...
written 11 weeks ago by Ben_Ensembl220
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Answer: A: How to retrieve COSMIC variations using Ensembl REST API?
... Hi Patrick, We seperate somatic data from germline, so the query should be: curl -H 'Content-type:text/xml' 'http://rest.ensembl.org/overlap/id/ENSG00000141510?feature=somatic_variation' COSMIC_MUTATION See: http://rest.ensembl.org/documentation/info/overlap_id for the list of featu ...
written 11 weeks ago by Ben_Ensembl220
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Answer: A: How do I get GO term annotations using VEP?
... Hello, The VEP GO.pm requires a database connection: https://github.com/Ensembl/VEP_plugins/blob/release/87/GO.pm Try using --database, rather than --cache. Best wishes Ben Ensembl Helpdesk ...
written 3 months ago by Ben_Ensembl220
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Answer: A: biomaRt GRCh37 down?
... Hello, There was a temporary disruption with the servers at the time you experienced this error message yesterday. Everything is running as it should be now. If you encounter any further errors (or are still encountering the same problem), please e-mail helpdesk@ensembl.org, and we will be able to ...
written 4 months ago by Ben_Ensembl220
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Answer: A: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... The problem with the mirror access here is that the URL should not have 'db' in the name. It should just read 'uswest.ensembl.org', 'useast.ensembl.org' or 'asia.ensembl.org'. ...
written 6 months ago by Ben_Ensembl220
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Answer: A: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... We're sorry to hear that you're still having problems- we're not entirely sure why you are not able to connect via the mirrors, as we have been able to replicate your error. Normal access will be restored on Tuesday 30th August. Sorry for any disruption caused. ...
written 7 months ago by Ben_Ensembl220

Latest awards to Ben_Ensembl

Scholar 6 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 6 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?
Scholar 4 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 6 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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