User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl930
Reputation:
930
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
12 hours ago
Joined:
3 years ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 58 results • page 1 of 6 • next >
4
votes
1
answer
79
views
1
answers
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 3 days ago by Ben_Ensembl930
2
votes
1
answer
108
views
1
answers
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 days ago by Ben_Ensembl930
6
votes
1
answer
108
views
1
answer
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 11 days ago by Ben_Ensembl930
4
votes
2
answers
93
views
2
answers
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 18 days ago by Ben_Ensembl930
0
votes
2
answers
227
views
2
answers
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 8 weeks ago by Ben_Ensembl930
1
vote
2
answers
227
views
2
answers
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 8 weeks ago by Ben_Ensembl930
2
votes
2
answers
227
views
2
answers
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 8 weeks ago by Ben_Ensembl930
2
votes
1
answer
225
views
1
answers
Comment: C: Assembly used in Variant Effect Predictor
... Hi Uday Rangaswarmy, I agree with the above posts, but would like to add that we also have the 'Assembly Convertor' tool to map coordinates from one assembly version to another: http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core Best wishes Ben ...
written 11 weeks ago by Ben_Ensembl930
1
vote
2
answers
269
views
2
answers
Comment: C: VEP output and stop gain mutation
... Hi Seta, No problem- very happy to help. There is no association between Condel scores and BLOSUM62 scores. Condel is a measure of amino acid substitution on protein function. It integrates the output of a number of computational tools aimed at assessing the impact of non synonymous SNVs on protein ...
written 3 months ago by Ben_Ensembl930
3
votes
2
answers
269
views
2
answers
Answer: A: VEP output and stop gain mutation
... Hi Seta, Since SIFT and Polyphen are predictions of the pathogenicity of amino acid substitution, SIFT and Polyphen scores are calculated for missense variants: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html The 'IMPACT' is a separate prediction, which is a subjectiv ...
written 3 months ago by Ben_Ensembl930

Latest awards to Ben_Ensembl

Scholar 3 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 3 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?
Scholar 9 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 17 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?
Scholar 18 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 8 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 3 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 4 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
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?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 5 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Popular Question 11 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 11 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 15 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 16 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 16 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 16 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 16 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 16 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 16 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?
Teacher 16 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?
Supporter 17 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 748 users visited in the last hour