Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl21k
Reputation:
20,600
Status:
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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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 5 months ago by Emily_Ensembl21k
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Comment: C: Make a GFF-file compatible for reference database
... try Mus_musculus.GRCm38.99.chr.gff3.gz ...
written 5 months ago by Emily_Ensembl21k
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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 5 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k
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Comment: C: convert 9million Marker Names to rsid
... Does it also have alleles? ...
written 6 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k
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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 6 months ago by Emily_Ensembl21k

Latest awards to Emily_Ensembl

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: misc_RNA in Ensembl
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: (Where) can I download the Ensembl cross reference database?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 5 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: How Do You Use Cloud Computing For Bioinformatics In 2013?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Librarian 5 months ago, created a post with more than 10 bookmarks. For How to apply for a job
Appreciated 5 months ago, created a post with more than 5 votes. For A: How Do You Use Cloud Computing For Bioinformatics In 2013?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Venter Genome Vcf
Scholar 5 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Scholar 6 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 6 months ago, created a question with more than 1,000 views. For Ensembl file formatting tool: tell us what you need
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 6 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 6 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 7 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Popular Question 7 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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