User: Ben_Ensembl

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Ben_Ensembl600
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EMBL-EBI
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@BENsembl
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Posts by Ben_Ensembl

<prev • 45 results • page 1 of 5 • next >
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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 3 months ago by Ben_Ensembl600
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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 3 months ago by Ben_Ensembl600
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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 3 months ago by Ben_Ensembl600
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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 3 months ago by Ben_Ensembl600
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Comment: C: VEP tools output
... No problem- very happy to help. You could do this using the --transcript_filter option, which uses similar notation and formatting as the filter_vep. For adding the zygosity, you can use the --individual option, but this only works with VCF files containing individual genotype data: https://www.en ...
written 3 months ago by Ben_Ensembl600
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Answer: A: VEP tools output
... Hi Nandini, 1. This is not possible using either the web interface or the standalone script. However, you can use a number of different filtering options, including --pick: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt or the filter_vep script to filter the VEP results ac ...
written 3 months ago by Ben_Ensembl600
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Answer: A: How to get Transcription End site (TES) via ensembl biomart ?
... Hello, You can't get transcription end site (TES) directly from BioMart, although as you pointed out, you can retrieve transcription start site (TSS) directly as a BioMart attribute. However, you can retrieve 'transcript start (bp)' and 'transcript end (bp)' as attributes from BioMart. You will ha ...
written 3 months ago by Ben_Ensembl600
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Answer: A: Invertebrate phylogenetic tree on Ensembl
... Hi, Invertebrate species are represented by the Ensembl Genomes project: http://ensemblgenomes.org The Ensembl genomes project is split into five divisions: plants, protists, fungi, non-vertebrate metazoans and bacteria. Ensembl Genomes produces phylogenetic trees for each taxa division, e.g: ht ...
written 7 months ago by Ben_Ensembl600
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Answer: A: How to retrieve Ensembl phenotype data associated with Ensembl variations using
... Hi Chilam, The script works when I run it on my machine with my own sample data. I used a test file with variants: rs991426868 0 phenotype records rs699 5 phenotype records rs2238612 1 phenotype record I suggest that the variant name is also output ($var->name), as a check fo ...
written 8 months ago by Ben_Ensembl600
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Comment: C: Reference and mutant allele of a SNP rsID
... Hi Deepak, I think you'd be most interested in the "allele_string" listed as C/T for this variant, for example: http://rest.ensembl.org/variation/human/rs56116432?content-type=application/json This is the reference allele / alternate allele. i.e C is the reference allele, T is the alternate allele ...
written 8 months ago by Ben_Ensembl600

Latest awards to Ben_Ensembl

Popular Question 3 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 7 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 8 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 8 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 8 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 8 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 8 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 9 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 15 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 19 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Appreciated 21 months ago, created a post with more than 5 votes. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016

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