User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl310
Reputation:
310
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
25 minutes ago
Joined:
1 year, 7 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 33 results • page 1 of 4 • next >
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Comment: 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 5 hours ago by Ben_Ensembl310
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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 6 hours ago by Ben_Ensembl310
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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 8 weeks ago by Ben_Ensembl310
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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 8 weeks ago by Ben_Ensembl310
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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 3 months ago by Ben_Ensembl310
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Comment: C: biomaRt getSequence() connection time-out
... Hi Flaviu, OK - please keep me updated how it goes. Best wishes Ben ...
written 3 months ago by Ben_Ensembl310
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Answer: A: biomaRt getSequence() connection time-out
... Hi Flaviu, We can't see anything wrong with your query or with biomaRt itself, so we think you might need to reduce the number of IDs per file from 50-60 to maybe 20 and see if this improve the problem. Sequences are quite heavy queries compared to just filtering on genes. Please do let me know how ...
written 3 months ago by Ben_Ensembl310
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Comment: C: LD calculation using LD plugin for VEP
... Hi Andrei, No, it's not possible to add 'distance' as an argument. For LD calculations, the default distance is 100Kb upstream and downstream of the focus variant. Best wishes Ben ...
written 4 months ago by Ben_Ensembl310
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Answer: A: What does *.* represent after Ensembl transcript name ?
... Hi Jack, The numbers after the '.' is versioning of the stable IDs. They represent minor changes to the underlying gene model, without having to re-assign a new stable ID. There is some more information in the Ensembl documentation pages: http://www.ensembl.org/info/genome/stable_ids/index.html B ...
written 5 months ago by Ben_Ensembl310
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Comment: C: LD calculation using LD plugin for VEP
... Hi Andrei, We would recommend https://www.cog-genomics.org/plink/2.0/ Best wishes Ben Ensembl Helpdesk ...
written 5 months ago by Ben_Ensembl310

Latest awards to Ben_Ensembl

Supporter 16 days ago, voted at least 25 times.
Scholar 8 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 6 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 6 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 10 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 12 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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