Emily_Ensembl
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BiomaRt error: Error in martCheck
9 votes

getSequence has only been enabled for the main Ensembl (vertebrates) biomaRt. This is all at the Bioconductor end. You'll need to use a getBM instead, for example: os_genes <- getBM(attributes =c("...

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Retrieve detailed gene descriptions
8 votes

Description of how to use biomaRt here. Filter by your list of gene IDs. Get the descriptions etc as attributes. Eg: > library(biomaRt) > ensembl = useEnsembl(biomart="ensembl", dataset="...

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Is there any difference between SNPs 'AG' and 'GA' in association analyses?
Accepted answer
8 votes

Could you please show us the context in which this appears, as you seem to be interpreting this differently to Devon. If it's appearing as you say, GA and AG, then Devon is right, this usually means ...

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Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?
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7 votes

If it's 3' incomplete that means the evidence used to create it was a fragment. Here's the evidence used to construct BRCA1-214 ENST00000477152.5, a 3' incomplete. You can see that there's a full ...

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Can exons be located outside of the coding sequence?
7 votes

Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.

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How to represent a deletion at position 1 in a VCF file?
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6 votes

From the latest VCF specs (page 8): REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of ...

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Why the gene symbol aliases have significantly different sequences?
5 votes

At Ensembl, we categorise synonyms as anything that a gene might also be known as. This includes older names for them, since those names will be in the literature, including where a gene has been ...

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How can I identify a recessive and dominant gene?
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5 votes

I'd probably look up the genes in OMIM, which provides detailed description of the functions and phenotypes associated with genes, including inheritance mode. For example, this is what you would get ...

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Protein sequence from patient data
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5 votes

Ensembl now have a tool called Haplosaurus (still in beta) which will convert your phased VCF into actual protein sequences. Haplosaurus haplo is a local tool implementation of the same ...

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What does 'Human Alternative sequence Gene' mean in Ensembl?
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4 votes

These are genes on the patches and haplotypes. Patches are repairs in the genome, where they have discovered the sequence or assembly is incorrect, so there is an alternative sequence that is created ...

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How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
4 votes

In your sequence header you will see: [location=complement(940023..940580)] It's a reverse strand gene. Reverse complement the sequence, then search the genome sequence.

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Ensembl protein identifiers from different assemblies
4 votes

Those IDs are elderly! Ensembl 54 was 2009! I would recommend using BioMart combined with the ID history converter. The ID history converter will convert old IDs to new, and BioMart will convert ...

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Is it possible to obtain RefSeq transcripts from Ensembl database for GRCh37 to match Ensembl Genes?
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4 votes

The RefSeq match option in BioMart is from the Matched Annotation from NCBI and EBI (MANE) collaboration between RefSeq and Ensembl. It has only been calculated for the up-to-date gene annotation on ...

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Getting species from ensembl sequence id
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4 votes

The lookup/id endpoint will get it for you. Of you can just look up the three letter species code, in this case MOD, on the list in the documentation.

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different results coming from biomart online and biomaRt R library
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4 votes

Sorry, this was my mistake in the last question. To search down the ontology, rather than just for the specific association with a term, biomaRt needs a different filter: 'go_parent_term'. Try: gene ...

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Are gene names same across species?
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4 votes

You could try using BioMart in Ensembl Metazoa. Filter by your list of gene names in honeybee, then get the fly homologues as attributes. The homologues are calculated by sequence comparison and ...

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Python API for working with ENSEMBL genomes
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4 votes

The correct API for Ensembl is the Ensembl REST API which is updated and maintained by Ensembl, and language agnostic.

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Keep Format and Individual fields when annotating VCF with VEP
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4 votes

The VEP TSV format can only keep in its own specified columns. If you want to maintain the data from your original input, get your output in VCF. It will add the VEP annotation to the INFO column, and ...

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Retrieval of genomic position by using biomaRt package
4 votes

BiomaRt cannot do that I'm afraid. There is an Ensembl REST API endpoint that will get you the genomic location of protein coordinates. It needs an Ensembl peptide ID an input though, so you could use ...

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Variant vs Allele vs SNP
3 votes

Variant = a locus in the genome where there are differences between individuals Allele = one of the possible bases/sequences that can occur at the variant SNP = single nucleotide polymorphism, a type ...

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Converting gene symbols between species
3 votes

Easiest way is BioMart. Help video to get you started here. Use the mouse genes dataset and filter by the list of gene names, get the mouse gene name and the human gene name (listed under homologues) ...

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1000 genomes missing SNPs on chr X in GRCh38
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3 votes

As I told you on 1000 genomes helpdesk: Because of the ploidy settings we used for our variant calling, we only called variants in the the pseudoautosomal region on the X chromosome. We are working on ...

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Where can I get ensembl Medaka genome for RNAseq
Accepted answer
3 votes

Download the ones without a chromosome number in the filename. Those files are the whole genome.

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VEP output SIFT_score unclear
3 votes

The dbNSFP plugin from VEP accesses tables of data for each variant from dbNSFP and pulls out the values. dbNSFP provide their SIFT scores in that format: a score for every transcript affected by the ...

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Retrieve all genes for a specific gene ontology
Accepted answer
3 votes

You can use BioMart to filter by your GO term and get the genes as attributes. BioMart is ontology-aware so will pull out all genes associated with your term and with any of its child terms. There is ...

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Understanding SNP coding for association analysis
Accepted answer
3 votes

Humans are diploid. This means they have two copies of each locus (with the exception of sex chromosomes in males). Your two alleles for each individual represent the two copies of this variant locus.

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Associating SNP and GENE
3 votes

Use the Variant Effect Predictor(VEP)

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HG19 Position meaning
2 votes

Yes, they are base pair positions

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How do population genetics people define a population?
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2 votes

It really depends on the study and the ethnicity. Mostly they use self-defined ethnicity and often they will require that three or four grandparents are of that ethnicity. Here's some detailed info on ...

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Find specific functional genes from a list?
2 votes

BioMart. Filter by your list of genes and a GO term linked to acetyl transferase activity.

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