User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl270
Reputation:
270
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
an hour ago
Joined:
1 year, 3 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 26 results • page 1 of 3 • next >
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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 11 days ago by Ben_Ensembl270
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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 4 weeks ago by Ben_Ensembl270
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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 6 weeks ago by Ben_Ensembl270
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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 6 weeks ago by Ben_Ensembl270
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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 7 weeks ago by Ben_Ensembl270
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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 7 weeks ago by Ben_Ensembl270
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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 8 weeks ago by Ben_Ensembl270
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Comment: C: LD calculation using LD plugin for VEP
... Hi Andrei, We think this might be because the HTS Library is missing. Try git clone --branch 1.3.2 --depth 1 https://github.com/samtools/htslib.git cd htslib make Set path HTSLIB_DIR=PATH_TO/htslib Hope this helps Best wishes Ben Ensembl Helpdesk ...
written 8 weeks ago by Ben_Ensembl270
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Answer: A: LD calculation using LD plugin for VEP
... Hello Andrei, We have updated the LD plugin, which should resolve the error you are encountering. Please get the latest version of the plugin from Github: https://github.com/Ensembl/VEP_plugins/blob/release/88/LD.pm Also, please be aware that you should use the specific 1000 Genomes populations (e ...
written 8 weeks ago by Ben_Ensembl270
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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 9 weeks ago by Ben_Ensembl270

Latest awards to Ben_Ensembl

Scholar 4 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 4 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 8 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 9 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 9 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 6 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 9 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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