User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl280
Reputation:
280
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
10 hours ago
Joined:
1 year, 5 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 29 results • page 1 of 3 • next >
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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 4 weeks ago by Ben_Ensembl280
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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 6 weeks ago by Ben_Ensembl280
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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 6 weeks ago by Ben_Ensembl280
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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 9 weeks ago by Ben_Ensembl280
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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 12 weeks ago by Ben_Ensembl280
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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 3 months ago by Ben_Ensembl280
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Comment: C: LD calculation using LD plugin for VEP
... Dear Andrei, If the LD-plugin encounters a connection problem, the VEP won’t report LD results for the variant and move on to the next variant and start LD computation again. The plugin hasn’t been frequently used and we can go back and revise the implementation. There might be a way of computing ...
written 3 months ago by Ben_Ensembl280
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Answer: A: LD calculation using LD plugin for VEP
... Hi Andrei, I'm just looking into this with my colleagues at the moment. I'll get back to you as soon as possible. Best wishes Ben ...
written 3 months ago by Ben_Ensembl280
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Comment: C: LD calculation using LD plugin for VEP
... Hi Andrei, It is not currently possible to run LD computation offline but it is something we can consider for future developments. As an alternative you could use the API for LD computation and compute LD in a region instead of doing a computation for each variant individually. http://www.ensembl.o ...
written 3 months ago by Ben_Ensembl280
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Comment: C: LD calculation using LD plugin for VEP
... Hi Andrei, LD computation is very time-consuming. We have pushed further speed improvements to https://github.com/Ensembl/VEP_plugins/tree/release/88 We advise that you should update the plugin and run again. We also recommend to use the new vep code for general speed improvements of the variant ...
written 3 months ago by Ben_Ensembl280

Latest awards to Ben_Ensembl

Scholar 12 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 12 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?
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 4 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 4 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 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 10 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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