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Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl ♦ 13k
Reputation:
12,660
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
8 minutes ago
Joined:
4 years, 7 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 • 836 results • page 1 of 84 • next >
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Comment: C: [hg19] Reading genes with CCDS
... Can you please give an example of a CCDS where it doesn't seem to match up. We can use this to try to work out what's going wrong. ...
written 1 day ago by Emily_Ensembl ♦ 13k
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Answer: A: SNP annotation with TFBS and histone marks
... The VEP will map your variants to TF motifs certainly, but there's currently no output that will give that will map to specific histone modifications. It will map your variants to regulatory features, such as promoters and enhancers, which are predicted based on TF binding, open chromatin and histon ...
written 4 days ago by Emily_Ensembl ♦ 13k
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Comment: C: refseq transcriptome annotation
... Why don't you just use GENCODE? ...
written 5 days ago by Emily_Ensembl ♦ 13k
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Answer: A: number of genes in human genome
... 20,338 protein coding genes on the primary assembly. 22,521 non-coding genes 14,638 pseudogenes = 56497 genes on the primary assembly On the [alternate assemblies][1] (haplotypes and patches): 2,750 protein coding 1,288 non-coding 1,600 pseudogenes = 5038 genes on the alternate assemblies. [Tota ...
written 5 days ago by Emily_Ensembl ♦ 13k
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Answer: A: Extract alignment blocks of a given region from MAF file having whole genome ali
... There is an [Ensembl REST API endpoint][1] that gets you alignments for a given region, but won't give you MAF as an output. [1]: http://rest.ensembl.org/documentation/info/genomic_alignment_region ...
written 6 days ago by Emily_Ensembl ♦ 13k
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Answer: A: Fetch Phenotypes from Orthologues and GO terms for a NonModel organism Gene Set
... You can do this by combining species datasets, see this [help page][1]. Use your non-model species as your first database then filter by IDs. Use the model species as your second dataset and get phenotypes and GO terms as attributes. [1]: http://www.ensembl.org/info/data/biomart/biomart_combinin ...
written 8 days ago by Emily_Ensembl ♦ 13k
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Comment: C: Annotate Ref/Alt for a list of rsIDs?
... How large is large? Give us a number. Also, I assume single species? ...
written 11 days ago by Emily_Ensembl ♦ 13k
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Comment: C: Cufflink, where is the raw gene count?
... I edited your title. One question mark is perfectly sufficient. ...
written 12 days ago by Emily_Ensembl ♦ 13k
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Comment: C: Using Terminal to Connect to Ensembl public MySQL Servers
... Are you getting some kind of error message with those commands? What is the error message? ...
written 14 days ago by Emily_Ensembl ♦ 13k
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Answer: A: Using Terminal to Connect to Ensembl public MySQL Servers
... That looks fine to me. Now you can just do normal MySQL queries by following the [schema here][1]. [1]: http://www.ensembl.org/info/docs/api/core/core_schema.html ...
written 14 days ago by Emily_Ensembl ♦ 13k

Latest awards to Emily_Ensembl

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 4 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Appreciated 26 days ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Appreciated 26 days ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 28 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: (Where) can I download the Ensembl cross reference database?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 28 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 4 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Making bioinformatics help and tutorials open
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
Scholar 7 weeks ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: What Do You Waste Your Time On
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Where To Find A Dna For Trying Out My Analysis On?
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 8 weeks 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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