Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl15k
Reputation:
15,430
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
49 minutes ago
Joined:
5 years, 7 months ago
Email:
e***********@gmail.com

Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).

Posts by Emily_Ensembl

<prev • 1,009 results • page 1 of 101 • next >
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Answer: A: Genomic coordinates from traditional HGVS variants
... You could try the [Ensembl VEP][1], which allows you to input a list of variants and gives you loads of information about them, including known rsIDs and genomic loci. HGVS is a valid VEP input. [1]: http://www.ensembl.org/Homo_sapiens/Tools/VEP?db=core ...
written 10 hours ago by Emily_Ensembl15k
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Comment: C: GRCh37.p13 download at NCBI FTP?
... No, you can't get it from ensemble, but you can get it from Ensembl. ...
written 1 day ago by Emily_Ensembl15k
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Answer: A: How to convert Ensembl ID to NCBI ID
... You want BioMart. Here is a [help video][1] to get you started. [1]: https://www.youtube.com/watch?v=QvGT2G0-hYA ...
written 1 day ago by Emily_Ensembl15k
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Comment: C: SNP rs ID batch query
... Variants do not have strand, which is why Ensembl adopt a default behaviour of always showing the forward strand alleles for all variants. The risk allele reported in papers is entirely dependant on what the paper authors decide to do, which may be the forward strand, may follow the strand of the al ...
written 2 days ago by Emily_Ensembl15k
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Comment: C: problem in getting results from variant effect predictor(VEP)
... I've sent it to our web-team, I'll go and bug them today. ...
written 4 days ago by Emily_Ensembl15k
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Answer: A: 1000 Genomes Project Reports Invalid Alleles for SNPs?
... According to [dbSNP][1], the C/T are the alleles on the reverse strand. All the 1000 Genomes alleles are reported on the forward strand, making GG homozygous reference. Please check the strand on the dataset you're using. [1]: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=499479 ...
written 7 days ago by Emily_Ensembl15k
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Comment: C: Keep Format and Individual fields after annotating VCF with VEP
... What are you trying to do with the data overall? Why is the data being in the CSQ field a problem? ...
written 8 days ago by Emily_Ensembl15k
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Comment: C: problem in getting results from variant effect predictor(VEP)
... There is a column in the jobs table called Ticket. It might be hidden. Click Show/hide columns then add ticket, and send the number that appears in the column with your email. It will help the team to find out what's going on with your job more easily. ...
written 9 days ago by Emily_Ensembl15k
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Answer: A: problem in getting results from variant effect predictor(VEP)
... I'm sorry you've had a problem. Please can you send the error message and your job number (from the jobs table) to helpdesk@ensembl.org. ...
written 9 days ago by Emily_Ensembl15k
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Answer: A: faster variant annotation for large VCFs
... There's some information about VEP speed in this [blog post](http://www.ensembl.info/2018/05/29/cool-stuff-the-vep-can-do-optimisation/). Your plugins are probably slowing you down a bit as they have to communicate with databases rather than using your offline cache, which can be slower – I'm afraid ...
written 15 days ago by Emily_Ensembl15k

Latest awards to Emily_Ensembl

Scholar 1 day ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Oracle 9 days ago, created more than 1,000 posts (questions + answers + comments).
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 17 days ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 6 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 9 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 10 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Scholar 10 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 11 weeks ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
Appreciated 3 months ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 3 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?

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