Moderator: Emily_Ensembl
Emily_Ensembl ♦ 15k
- 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
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... 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_Ensembl ♦ 15k
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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_Ensembl ♦ 15k
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... 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_Ensembl ♦ 15k
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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_Ensembl ♦ 15k
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... I've sent it to our web-team, I'll go and bug them today. ...
written 4 days ago by
Emily_Ensembl ♦ 15k
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... 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_Ensembl ♦ 15k
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... 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_Ensembl ♦ 15k
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109
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... 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_Ensembl ♦ 15k
0
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109
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... 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_Ensembl ♦ 15k
0
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136
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... 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_Ensembl ♦ 15k
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For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
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For C: How to write well in science, specially in bioinformatics ?
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For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
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created a post with more than 5 votes.
For C: How to write well in science, specially in bioinformatics ?
Good Answer
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created an answer that was upvoted at least 5 times.
For A: Venter Genome Vcf
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For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
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For A: (Where) can I download the Ensembl cross reference database?
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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
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For A: (Where) can I download the Ensembl cross reference database?
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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
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3 months ago,
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For C: How to write well in science, specially in bioinformatics ?
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For C: How to write well in science, specially in bioinformatics ?
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For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
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3 months ago,
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For A: (Where) can I download the Ensembl cross reference database?
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