User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl780
Reputation:
780
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
13 hours ago
Joined:
2 years, 10 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Assembly used in Variant Effect Predictor
... Hi Uday Rangaswarmy, I agree with the above posts, but would like to add that we also have the 'Assembly Convertor' tool to map coordinates from one assembly version to another: http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core Best wishes Ben ...
written 19 days ago by Ben_Ensembl780
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Comment: C: VEP output and stop gain mutation
... Hi Seta, No problem- very happy to help. There is no association between Condel scores and BLOSUM62 scores. Condel is a measure of amino acid substitution on protein function. It integrates the output of a number of computational tools aimed at assessing the impact of non synonymous SNVs on protein ...
written 4 weeks ago by Ben_Ensembl780
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Answer: A: VEP output and stop gain mutation
... Hi Seta, Since SIFT and Polyphen are predictions of the pathogenicity of amino acid substitution, SIFT and Polyphen scores are calculated for missense variants: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html The 'IMPACT' is a separate prediction, which is a subjectiv ...
written 4 weeks ago by Ben_Ensembl780
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Comment: C: ENSEMBL annotation file for quantification: which file to use?
... Sure- I'll talk with my colleagues who are responsible for the README file and see whether we can update it to make it more comprehensive. ...
written 11 weeks ago by Ben_Ensembl780
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Answer: A: ENSEMBL annotation file for quantification: which file to use?
... Just to compliment Devon Ryan's answer: .gtf: This is the default file, it should contain the full annotation for all species except human and mouse. For human and mouse, it will contain all annotation on the primary assembly, ie excluding patch and haplotype regions. All species have one. .chr.gt ...
written 11 weeks ago by Ben_Ensembl780
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Answer: A: Species not in Ensembl
... Hi Ruben, For an organism to be included in Ensembl Metazoa (https://metazoa.ensembl.org), the genome needs to be in INDSC, with annotation. Having spoken to my colleagues, it looks like this organism has both a reasonable quality assembly and annotation at the NCBI - so it’s a candidate we'd be ...
written 3 months ago by Ben_Ensembl780
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Comment: C: VEP tools output
... Hi Nandini, My colleagues have said that they are currently helping you on GitHub: https://github.com/Ensembl/ensembl-vep/issues/150#issuecomment-371137459 For this error, it's best that they help you. Best wishes Ben Ensembl Helpdesk ...
written 9 months ago by Ben_Ensembl780
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Answer: A: VEP tools output
... Hi Nandini, I'm glad to hear that. You will need to use filter_vep using the following guidelines: http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html#filter_write Best wishes Ben Ensembl Helpdesk ...
written 9 months ago by Ben_Ensembl780
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Answer: A: Finding zebrafish promoters ENSEMBL
... Hi Seigfried, Step 1: Choose Database - Ensembl Genes 91 Choose Dataset - Zebrafish genes (GRCz10) Step 2: Click 'Filters' in the menu on the left hand side. Expand 'Gene' panel. Check the 'Input external references ID list' box to add the filter and add the list of gene IDs into the text box ( ...
written 9 months ago by Ben_Ensembl780
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Comment: C: Finding zebrafish promoters ENSEMBL
... Hi Seigfried, You are right in that regulatory feature annotation is only available for human and mouse in Ensembl at the moment. However, regulatory features are annotated independently of genes, and are not directly linked, anyway. If you are interested in retrieving the 2kb upstream sequence th ...
written 9 months ago by Ben_Ensembl780

Latest awards to Ben_Ensembl

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 3 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Popular Question 9 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Supporter 15 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 19 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 21 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?

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