Moderator: Emily_Ensembl
Emily_Ensembl ♦ 21k
- Reputation:
- 20,600
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- Trusted
- Location:
- EMBL-EBI
- Website:
- http://www.ensembl.org...
- Twitter:
- @Ensemily
- Last seen:
- 2 months, 1 week ago
- Joined:
- 7 years, 6 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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... Sorry, I put in the wrong thing. Edited my comment now. I meant the one with chr in the name, that should be *just* the primary assembly. ...
written 5 months ago by
Emily_Ensembl ♦ 21k
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... try Mus_musculus.GRCm38.99.chr.gff3.gz ...
written 5 months ago by
Emily_Ensembl ♦ 21k
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... Which GFF file are you using from Ensembl? If you use the chr_patch_hapl_scaff file this will contain duplicated gene names due to the genes on the [patches and haplotypes](http://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html). Could this be the problem? ...
written 5 months ago by
Emily_Ensembl ♦ 21k
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... Search for the gene and go to Variant table in the menu on the left. [For example.][1]
[1]: http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000108055;r=10:110567691-110604636 ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... Easiest thing is to stick the variants into the [Ensembl VEP](https://www.ensembl.org/info/docs/tools/vep/index.html). It will calculate the consequences on genes and give you rsIDs of known variants at the loci. ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... Is this with a REST endpoint? Given this [REST input](http://rest.ensembl.org/vep/human/id/rs699?content-type=application/json), here's what I get under frequencies:
frequencies: {
G: {
eur: 0.4115,
gnomad_amr: 0.7196,
gnomad_oth: 0.5002,
gnomad_afr: 0.8451 ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... Does it also have alleles? ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... The INFO column fills in consequences of the variant on known gene. If there is no variant, there is no consequence so nothing to fill in. All `--allow_no_variant` does is keep it in the VCF output. ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: 2 years
Grading: Grade 4 (starts at £2,483 net monthly) or Grade 5 (starts at £2,676 net monthly)
Closing Date: 5 March 2020
Reference Number: EBI01580
Ensembl-HAVANA produces a reference gene a ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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... We're in contact with the authors and trying to push them. ...
written 6 months ago by
Emily_Ensembl ♦ 21k
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