User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl270
Reputation:
270
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
14 hours ago
Joined:
1 year, 2 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 25 results • page 1 of 3 • next >
3
votes
2
answers
78
views
2
answers
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 1 day ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 14 days ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 14 days ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 19 days ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 21 days ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 25 days ago by Ben_Ensembl270
0
votes
2
answers
179
views
2
answers
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 25 days ago by Ben_Ensembl270
2
votes
2
answers
179
views
2
answers
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 26 days ago by Ben_Ensembl270
1
vote
2
answers
173
views
2
answers
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 weeks ago by Ben_Ensembl270
3
votes
1
answer
127
views
1
answers
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 5 weeks ago by Ben_Ensembl270

Latest awards to Ben_Ensembl

Scholar 1 day ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 1 day 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 26 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 7 months ago, created a post with more than 5 votes. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 968 users visited in the last hour