Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl16k
Reputation:
16,450
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
an hour ago
Joined:
5 years, 11 months ago
Email:
e***********@gmail.com

Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).

Posts by Emily_Ensembl

<prev • 1,091 results • page 1 of 110 • next >
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Answer: A: Conserv CSQ and output plugin
... The reason you're losing the MaxEntScan fields is that you didn't specify them with --fields. You can run without --fields and you'll get the data, or you can run with it and specify the MaxEntScan fields too. ./vep -i input.vcf -o output.vcf --plugin MaxEntScan,/data2/MaxEntScan/fordownload -v ...
written 2 hours ago by Emily_Ensembl16k
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Comment: C: Conserv CSQ and output plugin
... Tagging me doesn't do anything. ...
written 5 hours ago by Emily_Ensembl16k
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Answer: A: How to map SNP rsids to genes and flanks
... Use [Ensembl BioMart](http://www.ensembl.org/biomart/martview/d105a3cc610a50f5b176fda117f5340f). Use the gene database, filter by the gene names and get the variants as attributes. Here's a [help video](https://www.youtube.com/watch?v=QvGT2G0-hYA) to get you started with BioMart. Alternatively, [En ...
written 1 day ago by Emily_Ensembl16k
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Answer: A: Data changes between reference assemblies
... A specific thing they looked to do for GRCh38 was identify variants where the reference base was a rare or private allele. Since the genome is made up contigs, all of which are sequenced from real people's genomes and those people have rare or private alleles in their genomes, these will occur in th ...
written 8 days ago by Emily_Ensembl16k
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Answer: A: BiomaRt: archive version of ensembl not working
... Try: > mart=useMart("ensembl",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl") ...
written 9 days ago by Emily_Ensembl16k
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Comment: C: Using VEP to get gnomAD frequencies
... Yes, I think that standard convention states that VCF should have only forward strand alleles. Perhaps this is something to raise with COSMIC if they are putting reverse strand alleles in their VCFs. ...
written 14 days ago by Emily_Ensembl16k
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Comment: C: Ensembl Multiple Genome alignments sequence genome coordinate
... Can you please give us some examples of regions where this does not match. ...
written 15 days ago by Emily_Ensembl16k
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Answer: A: Using VEP to get gnomAD frequencies
... The reference allele, in this case, appears to be a very rare allele. The reference allele is whatever was found in the reference genome, which is a genomic region of a real person, which means that it can be a rare or private allele. In this case, the reference, A, is very rare. The VEP is giving ...
written 15 days ago by Emily_Ensembl16k
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News: Free online Ensembl REST API training
... We've just launched a new free online training course on using the [Ensembl REST APIs](https://www.ebi.ac.uk/training/online/course/ensembl-rest-api) to access genomic data. The course uses interactive online Jupyter notebooks on Microsoft Azure, which are available in Python, Perl and R. This is t ...
jupyter python news rest api perl ensembl written 4 weeks ago by Emily_Ensembl16k
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... To filter by GO IDs you have to use the filter for GO IDs. If you're just looking to get genes associated with those exact terms, use `go`, if you want to get the genes associated with all their child terms too, use `go_parent_term`. ...
written 4 weeks ago by Emily_Ensembl16k

Latest awards to Emily_Ensembl

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 7 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
Appreciated 29 days ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Scholar 4 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Appreciated 4 weeks ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 5 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 6 weeks ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 7 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
Scholar 7 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
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?
Scholar 12 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Popular Question 3 months ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
Appreciated 3 months ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Appreciated 3 months ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl

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