Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl21k
Reputation:
20,760
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
13 hours ago
Joined:
7 years, 8 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

<prev • 1,344 results • page 1 of 135 • next >
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News: Get Ensembl training, virtually
... You’re invited to join us for a free, open, virtual training course, 30th November – 2nd December. The course will be held using the Blackboard training platform. ## Who is this course for? This course is for anyone who would to learn more about using Ensembl via the browser through webinar videos ...
ensembl online news training written 2 days ago by Emily_Ensembl21k
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Answer: A: retrieve matched genome/annotation pairs using Ensembl API
... The Ensembl REST API is not designed for anything like that. It should be relatively easy to use the standard paths on the FTP site to script a wget download. You may find it useful to use the [info/genomes/division endpoint](https://rest.ensembl.org/documentation/info/info_genomes_division) from th ...
written 3 days ago by Emily_Ensembl21k
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Comment: C: getBM error while using bioMart
... This is correct. There are https changes and we're attempting to get this fixed today. ...
written 14 days ago by Emily_Ensembl21k
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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 8 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 8 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 8 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 8 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 8 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 8 months ago by Emily_Ensembl21k
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Comment: C: convert 9million Marker Names to rsid
... Does it also have alleles? ...
written 8 months ago by Emily_Ensembl21k

Latest awards to Emily_Ensembl

Scholar 3 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Popular Question 11 days ago, created a question with more than 1,000 views. For Free Ensembl courses
Appreciated 28 days ago, created a post with more than 5 votes. For A: Venter Genome Vcf
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Venter Genome Vcf
Scholar 4 months ago, created an answer that has been accepted. For A: misc_RNA in Ensembl
Scholar 4 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Popular Question 4 months ago, created a question with more than 1,000 views. For Ensembl eHive Software developer
Popular Question 4 months ago, created a question with more than 1,000 views. For Gene annotation project leader at Ensembl
Popular Question 4 months ago, created a question with more than 1,000 views. For Post tagging etiquette musings
Popular Question 4 months ago, created a question with more than 1,000 views. For Free Ensembl courses
Great Question 4 months ago, created a question with more than 5,000 views. For The Ensembl Vep For Easy Analysis Of Your Variants
Appreciated 4 months ago, created a post with more than 5 votes. For A: Venter Genome Vcf
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: misc_RNA in Ensembl
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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?
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Scholar 8 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Scholar 8 months ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?

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