User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl1.0k
Reputation:
1,010
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Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
2 days, 6 hours ago
Joined:
3 years, 4 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 61 results • page 1 of 7 • next >
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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 3 days 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 5 weeks 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 11 weeks 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 4 months ago by Ben_Ensembl1.0k
2
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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 4 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 4 months ago by Ben_Ensembl1.0k
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Answer: A: Missing transcripts (ENST numbers) in gff3 files from the ENSEMBL ftp site
... Hi goldberg.jm, The transcript you gave as an example is located on an assembly exception (see 'location' in the link below): https://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000232960;r=CHR_HSCHR6_MHC_MANN_CTG1:31705518-31709524;t=ENST00000454382 The FTP directory contains a number ...
written 4 months ago by Ben_Ensembl1.0k
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Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
... Yes, the link you gave is the correct link to download the top-level sequences: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz ...
written 5 months ago by Ben_Ensembl1.0k
1
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Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
... No problem- very happy to help. All alternative assembly and patch regions have their sequence padded with N's to ensure alignment programs can report the correct index regions. ...
written 5 months ago by Ben_Ensembl1.0k
2
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414
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Answer: A: Which Ensembl chromosome sequence file is used for the gff3 files?
... Hi O.rka, The GFF3 file contains all annotated features on all sequences, including chromsomes, regions not assembled into chromosomes and haplotype/patch regions. Therefore, the corresponding FASTA files will be one of the toplevel files here: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_s ...
written 5 months ago by Ben_Ensembl1.0k

Latest awards to Ben_Ensembl

Guru 2 days ago, received more than 100 upvotes.
Teacher 2 days 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 15 days ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 3 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
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 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 4 months 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 7 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 8 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 8 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 9 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 9 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?
Popular Question 15 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 19 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 20 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 20 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 20 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms

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