Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl20k
Reputation:
20,420
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
1 month ago
Joined:
7 years, 1 month 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

<prev • 1,341 results • page 1 of 135 • next >
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Comment: C: Make a GFF-file compatible for reference database
... 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 7 weeks ago by Emily_Ensembl20k
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Comment: C: Make a GFF-file compatible for reference database
... try Mus_musculus.GRCm38.99.chr.gff3.gz ...
written 7 weeks ago by Emily_Ensembl20k
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Comment: C: Make a GFF-file compatible for reference database
... 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 7 weeks ago by Emily_Ensembl20k
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Answer: A: How to collect all SNPs data of specific gene from Ensembl database?
... 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 8 weeks ago by Emily_Ensembl20k
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Answer: A: convert 9million Marker Names to rsid
... 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 9 weeks ago by Emily_Ensembl20k
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Answer: A: "gnomad_allele" field in new VEP
... 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 9 weeks ago by Emily_Ensembl20k
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Comment: C: convert 9million Marker Names to rsid
... Does it also have alleles? ...
written 9 weeks ago by Emily_Ensembl20k
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Answer: A: Adding consequences field (INFO) when using --allow_non_variant in VEP
... 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 10 weeks ago by Emily_Ensembl20k
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Job: Ensembl Genome Annotator (Regulation)
... 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 ...
ensembl job annotation written 10 weeks ago by Emily_Ensembl20k
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Comment: C: What to do to include data from strawberry in Biomart Ensembl
... We're in contact with the authors and trying to push them. ...
written 10 weeks ago by Emily_Ensembl20k

Latest awards to Emily_Ensembl

Scholar 5 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Scholar 8 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Ensembl file formatting tool: tell us what you need
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 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?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 11 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 12 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Popular Question 3 months ago, created a question with more than 1,000 views. For Ensembl file formatting tool: tell us what you need
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?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Venter Genome Vcf
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Help obtaining splice site data from dbSNP!
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: misc_RNA in Ensembl
Scholar 3 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 4 months ago, created a question with more than 1,000 views. For Ensembl file formatting tool: tell us what you need

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