User: Erin_Ensembl

gravatar for Erin_Ensembl
Erin_Ensembl370
Reputation:
370
Status:
Trusted
Location:
EMBL-EBI
Website:
http://www.ensembl.info/
Twitter:
@mycoacia
Last seen:
3 weeks ago
Joined:
1 year, 11 months ago
Email:
e*******@ebi.ac.uk

 

 

 

Posts by Erin_Ensembl

<prev • 35 results • page 1 of 4 • next >
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Answer: A: hg38 Ig regions
... You can use Ensembl's [BioMart][1] tool. 1. Choose **Ensembl Genes** 2. Choose **Human genes (GRCh38p.12)** 3. Click on **Filters**, expand GENE, scroll down to find biotype and choose all the IG genes. If you're only interested in the primary assembly (excluding haplotypic regions and ...
written 3 months ago by Erin_Ensembl370
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Answer: A: Extract Ensembl IDs column using a data file
... BioMart is definitely the way to go. You can use the R package Bioconductor as c.chakraborty suggests, or the point and click web tool. We have a [video][1] covering ID conversion that you may find helpful. [1]: https://www.youtube.com/watch?v=OIAuBoUPOHw ...
written 3 months ago by Erin_Ensembl370
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Comment: C: Annovar annotation for plants
... I suspect that it might be a problem with the gene annotation file (GTF) being recognised. Can you send an email to Helpdesk [at]ensembl.org so we can take a look in more detail? ...
written 4 months ago by Erin_Ensembl370
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Answer: A: How and where can I submit functional information that I created for an already
... If you have annotations for gene functions, then you may want to consider submitting them to the [Gene Ontology][1] resource. There are details on how to submit and what the requirements for submission are on their [FTP][2] site. I do not know if they require the data to be published or not. Depend ...
written 4 months ago by Erin_Ensembl370
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hey, The full list of variant consequences annotated by the VEP are [here][1]. So missense variants will give you SNPs that change the amino acid within the protein, this may be serious for protein function and structure, or not, depending on the chemical properties and conservation of that amino a ...
written 4 months ago by Erin_Ensembl370
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hello, You can only do this if you have annotated your VCF with consequence terms, which are listed in the INFO field. Looking at your previous example it looks like you don't. This is an example of what it might look like: 8 38144352 rs551783234 A G . . CSQ=G|missense_variant|MODERATE|STAR|E ...
written 4 months ago by Erin_Ensembl370
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Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... Hello aammarah.632 All of the above suggestions are great - BioMart will work with versioned IDs but you need to select the correct format, and if they are not existing in the current database (regardless of the version) then no results will be found. I took a look at a couple of your IDs, I can ...
written 4 months ago by Erin_Ensembl370
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... No problem! If you decide you want to use the VEP in the future, you can get around the uploading the VCF by using the VEP script/Perl API. If you install the [cache][1] (available for hg19/GRCh37) then you can run the analysis locally and [offline][2], hence you don't need to worry about the data ...
written 4 months ago by Erin_Ensembl370
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Comment: C: Is there a data base, tool or method I can use to find out which of my genes cod
... The GO site has a GO enrichment analysis tool found on their [homepage][1], so you can just pop in your IDs and see the mapped terms. I think you can then filter the dataset to see specific terms. Seems like an easier way than matching up lists. It also has options to export in a range of formats an ...
written 4 months ago by Erin_Ensembl370
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Yes indeed, thanks Finswimmer. Depending on what you're doing in your analysis you might want to use VEP rather than BCF tools. In using the VEP you can apply filters based on the gene IDs or names, rather than specifying the genomic coordinate which could save you the extra step. You'd also gain ...
written 4 months ago by Erin_Ensembl370

Latest awards to Erin_Ensembl

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: problem in EnsemblID to gene symbol conversion in TCGA data
Appreciated 3 months ago, created a post with more than 5 votes. For A: Fasta file and GTF file for STAR alignment
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Fasta file and GTF file for STAR alignment
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Fasta file and GTF file for STAR alignment
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Fasta file and GTF file for STAR alignment
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Fasta file and GTF file for STAR alignment

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