Moderator: Emily_Ensembl

gravatar for Emily_Ensembl
Emily_Ensembl14k
Reputation:
14,470
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.org...
Twitter:
@Ensemily
Last seen:
22 minutes ago
Joined:
5 years, 3 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 • 946 results • page 1 of 95 • next >
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Forum: How do you use BLAST?
... We're looking into whether we can make improvements to [Ensembl BLAST/BLAT](http://www.ensembl.org/Multi/Tools/Blast?db=core) so want to find out about how people use sequence searching tools. Please can you tell us: * What your aims are when you BLAST/BLAT a sequence. * What you do with your BLAST ...
forum blast sequence searching blat written 4 days ago by Emily_Ensembl14k • updated 3 days ago by Vijay Lakhujani2.1k
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Comment: C: BioMart: connection fails
... Archives are now back. ...
written 4 days ago by Emily_Ensembl14k
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Answer: A: BioMart: connection fails
... The archive sites are currently down due to disk problems. We're currently working on getting them fixed. ...
written 4 days ago by Emily_Ensembl14k
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... If you're working with human, mouse or zebrafish, any duplicated gene names with multiple Ensembl gene IDs are likely to be down to patches and haplotypes, which are alternative versions of genomic regions. We have a [help video](https://www.youtube.com/watch?v=sPE9j_Hw9HU) explaining these. Many pe ...
written 8 days ago by Emily_Ensembl14k
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Comment: C: VEP annotation doubt with NM (NM_000000.1_dup19)
... There's 36 of them in the up-to-date database, so it's not universal. For various historical and political reasons, we have have two different snapshots of the RefSeq database which we merge together, so it will only be things that have been updated between those two snapshots. ...
written 17 days ago by Emily_Ensembl14k
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Comment: C: VEP annotation doubt with NM (NM_000000.1_dup19)
... We've uncovered the source. This occurs in our pipeline that import the RefSeq transcripts. If we find that there are two with the same ID (eg NM_001170637.3 and NM_001170637.2), the pipeline is adding this dupl suffix, instead of the sensible option of just deleting the older one. We're not sure wh ...
written 17 days ago by Emily_Ensembl14k
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Answer: A: snp annotation using BiomaRt
... As Wouter says, BioMart is not really a suitable tool for this as it cannot handle that much data. The [Variant Effect Predictor (or VEP)](http://www.ensembl.org/info/docs/tools/vep/index.html) can, however take millions of variants and output for you which genes they hit and what effects they have. ...
written 18 days ago by Emily_Ensembl14k
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Comment: C: quality trimming with trimmomatic
... I'd like to clarify this a little further and tell you about how I deal with representing a (free) resource on here. The first thing you'll see is my name "Emily Ensembl" – I've made it completely obvious that I work for Ensembl, this is my disclaimer. Everybody knows that when I recommend Ensembl ...
written 18 days ago by Emily_Ensembl14k
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Answer: A: VEP transcript CDS lenght
... I'll speak to our variation team about getting these added to the VEP output, maybe as an optional extra. ...
written 19 days ago by Emily_Ensembl14k
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Answer: A: VEP annotation doubt with NM (NM_000000.1_dup19)
... We are investigating these. It looks like some RefSeq transcripts (eg NM_001170637.3) have been duplicated in Ensembl's other_features database with a lower version number and this dupl suffix (eg NM_001170637.2_dupl3). This has been propagated across to the VEP cache, which is why you're seeing the ...
written 19 days ago by Emily_Ensembl14k

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 5 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: (Where) can I download the Ensembl cross reference database?
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Popular Question 17 days ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
Appreciated 17 days ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Commentator 17 days ago, created a comment with at least 3 up-votes. For C: How to write well in science, specially in bioinformatics ?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Good Answer 18 days ago, created an answer that was upvoted at least 5 times. For A: Venter Genome Vcf
Appreciated 19 days ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Scholar 19 days ago, created an answer that has been accepted. For A: misc_RNA in Ensembl
Scholar 19 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 20 days ago, created an answer that has been accepted. For A: (Where) can I download the Ensembl cross reference database?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: What Is A "Gene"? Redundancies In Refseq Versus Ensembl
Scholar 20 days 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
Popular Question 7 weeks ago, created a question with more than 1,000 views. For ENCODE Users' Meeting
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 ENCODE Users' Meeting
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?
Appreciated 3 months ago, created a post with more than 5 votes. For C: How to write well in science, specially in bioinformatics ?
Popular Question 3 months ago, created a question with more than 1,000 views. For ENCODE Users' Meeting

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