Moderator: Emily_Ensembl
Emily_Ensembl ♦ 21k
- Reputation:
- 20,960
- Status:
- Trusted
- Location:
- EMBL-EBI
- Website:
- http://www.ensembl.org...
- Twitter:
- @Ensemily
- Last seen:
- 8 minutes ago
- Joined:
- 7 years, 11 months ago
- Email:
- e****@ebi.ac.uk
Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).
(she/her/hers)
Posts by Emily_Ensembl
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... The VEP considers all transcripts annotated by Ensembl. ...
written 5 days ago by
Emily_Ensembl ♦ 21k
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... Click on "Configure this page" then add all the tracks and legends you want to see. ...
written 29 days ago by
Emily_Ensembl ♦ 21k
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... This is down to a particular quirk of HGVS in right shifting any deletions/insertions which have the same outcome. The location in the CDS of your input deletion region is 607-613, whereas the HGVS shows it to be 612-618. The sequence of this region is:
607 - TGCTGCGTGCTGA - 619
C C ...
written 5 weeks ago by
Emily_Ensembl ♦ 21k
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... We have it on our list of genomes to add but we're waiting for the latest 2020 version to be given a GCA accession by the INSDC, as this is a [requirement for us](http://www.ensembl.org/info/about/legal/browser_agreement.html).
If you want to annotate your variants, you can still do so using the [E ...
written 6 weeks ago by
Emily_Ensembl ♦ 21k
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Comment:
C: How to annotate Missing Positions
... What information do you have? ...
written 7 weeks ago by
Emily_Ensembl ♦ 21k
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... `host = "https://plants.ensembl.org"` ...
written 7 weeks ago by
Emily_Ensembl ♦ 21k
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... The alleles of the variant are A/G, the alleles in the gene are T/C. When referring only to the variant, the convention is to always talk about the forward strand allele. The papers you are referring to are using the alleles in the gene. ...
written 9 weeks ago by
Emily_Ensembl ♦ 21k
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... A (or T if you're talking about the gene) is the reference allele. That means it is the allele that is found on the reference genome.
The major allele is G. This is the most frequent allele in the [1000 Genomes](http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=7:87549785-87550785; ...
written 9 weeks ago by
Emily_Ensembl ♦ 21k
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Answer:
A: VEP repeated region flag
... We haven't got any plugins to check repeat regions, I'm afraid. If you have a suitable bed file you can use the [custom annotations](http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html) options, but we don't release bed files of the repeats. ...
written 9 weeks ago by
Emily_Ensembl ♦ 21k
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... Don't use BioMart, use the [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) instead. ...
written 11 weeks ago by
Emily_Ensembl ♦ 21k
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