User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl720
Reputation:
720
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
1 day, 4 hours ago
Joined:
2 years, 8 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 48 results • page 1 of 5 • next >
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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 22 days ago by Ben_Ensembl720
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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 22 days ago by Ben_Ensembl720
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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 7 weeks ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720
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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 7 months ago by Ben_Ensembl720

Latest awards to Ben_Ensembl

Appreciated 19 days ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 22 days 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 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 7 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 7 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?
Popular Question 7 months ago, created a question with more than 1,000 views. For Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 11 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 12 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 12 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 12 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 12 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 12 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 12 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 12 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 13 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 18 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 18 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 18 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 23 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?

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