User: Ben_Ensembl

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Ben_Ensembl1.0k
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EMBL-EBI
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@BENsembl
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1 day, 10 hours ago
Joined:
3 years, 9 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Microarray Probe IDs to ENSEMBL ID
... Hi, No problem. Individual probes are approx. 25 bp in length and are grouped together to form probesets. The individual probes can be used in different probesets to assess the expression of more than one gene, since the 25bp sequence can map to more than one region in the genome. Best wishes Ben ...
written 6 weeks ago by Ben_Ensembl1.0k
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Comment: C: Microarray Probe IDs to ENSEMBL ID
... Hi, Could you share you biomaRt query? ...
written 6 weeks ago by Ben_Ensembl1.0k
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Answer: A: Microarray Probe IDs to ENSEMBL ID
... Hi Scott McKay, In the annotation process, Ensembl annotates transcripts and groups them together to form genes. We use stable IDs for all of our annotated transcripts and genes (and other annotated features too). We use ENSG# IDs for human genes, and ENST# IDs for human transcripts. There is furth ...
written 7 weeks ago by Ben_Ensembl1.0k
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Answer: A: Homology in EMBL Biomart
... Hi The Last Word, In Ensembl, homologues are inferred from the gene trees we produce as part of our comparative genomics analyses: http://www.ensembl.org/info/genome/compara/homology_method.html We do not use known/curated lists of homologous genes in our predictions. Best wishes Ben Ensembl Hel ...
written 4 months ago by Ben_Ensembl1.0k
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Answer: A: IMPACT rating in VEP and compatibility with which tools?
... Hi Shicheng Guo, The IMPACT descriptions correspond to [Sequence Ontology][1] terms which describe predicted variant consequences. The table in the following documentation lists all SO terms and the corresponding IMPACT rating used in Ensembl: http://www.ensembl.org/info/genome/variation/prediction ...
written 5 months ago by Ben_Ensembl1.0k
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Answer: A: Ensembl variant effect predictor fails if REF or ALT allele has a length around
... Hi mo.imranshah, There are difficulties in handling long allele strings (>1000bp) for variants in VEP when fetching everything that overlaps the allele string and probably this was what lead to the fork failing. We plan to look more into it to figure out exactly what would be an 'upper limit' a ...
written 6 months ago by Ben_Ensembl1.0k
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Answer: A: query and export SNPs information from ensembl
... Hi Vincenzo, I would advise using the Ensembl REST API: https://rest.ensembl.org You can use the POST variation:/species/ endpoint using the pops optional parameter: https://rest.ensembl.org/documentation/info/variation_post Best wishes Ben Ensembl Helpdesk ...
written 7 months ago by Ben_Ensembl1.0k
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Answer: A: Timeout on getBM() to retrieve snps from locations
... Hi Corentin, Since this query is too large for BioMart, I would suggest using the Ensembl REST API Overlap endpoint, restricting the query using the 'feature=variation' parameter: https://rest.ensembl.org/documentation/info/overlap_region e.g https://rest.ensembl.org/overlap/region/human/7:1404249 ...
written 9 months ago by Ben_Ensembl1.0k
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Answer: A: Temporarily reduced functionality of Ensembl and Ensembl Genomes
... The recent issues affecting Ensembl and Ensembl Genomes have now been resolved and all services are back to normal. Thank you for your patience while we got everything back up and running. If you do experience any errors, please contact the [Ensembl Helpdesk][1]. Best wishes Ensembl Helpdesk ...
written 9 months ago by Ben_Ensembl1.0k
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News: Temporarily reduced functionality of Ensembl and Ensembl Genomes
... Ensembl and Ensembl Genomes are currently experiencing reduced functionality due to a major incident at one of our data centres leading to many of our internal services being shutdown, with services disrupted from Friday 1st February. Currently off line are the web versions of most Ensembl tools ( ...
ensembl news written 9 months ago by Ben_Ensembl1.0k

Latest awards to Ben_Ensembl

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?
Guru 5 months ago, received more than 100 upvotes.
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?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 8 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 12 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?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 13 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?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 14 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 14 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?
Popular Question 20 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 24 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?
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 2.1 years ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 2.1 years 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?

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