Skip to main content

Questions tagged [biomart]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
1 answer
45 views

Gene ensemble vs Hugo id

Hi I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
ToTheMoon's user avatar
0 votes
1 answer
37 views

Chromosome position -> ENSP

I'd like a tabix file that, for every position in the genome, gives me a list of every ENSP within 5kb of that position. This should be easy right... I know VEP /kinda/ gives me this, but I'd rather ...
Dan Bolser's user avatar
3 votes
1 answer
42 views

biomarRT conversion of symbols

I wanted to use the code to convert mouse to human symbol, but I have problem with the mirror, I've tried to establish another one, but continue to have the same problem. ...
María José's user avatar
1 vote
1 answer
277 views

Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs: ...
An Ignorant Wanderer's user avatar
1 vote
1 answer
214 views

What does the "filters" argument in "getBM" do?

In the biomaRt package, there is a function getBM which among a few things is useful for mapping between different gene ...
An Ignorant Wanderer's user avatar
0 votes
1 answer
154 views

Calculating dn/ds ratio between two model organisms

I am trying to calculate the dn/ds ratio between the human genes and c.elegans. However, I am getting NA values in the output file I used the following script ...
Tom Morgan's user avatar
0 votes
1 answer
197 views

Getting all promoters of a specific gene

I'd like to perform a motif analysis of all promoter regions of the gene ENSMUSG00000020538 in mus musculus. To do so, I wanted to use Biomart : ...
user1595929's user avatar
1 vote
1 answer
516 views

Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
nano's user avatar
  • 11
1 vote
0 answers
151 views

How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
user345394's user avatar
1 vote
1 answer
285 views

Too slow issue of BioMart

I am using library(biomaRt) in R to annotate SNP rsid. It takes too much time for only 1000 SNPs....... I would like to know how I can run this code faster. ...
user224050's user avatar
0 votes
2 answers
362 views

Problem with merge data while trying to convert gene names in R

This question has also been asked on Biostars and StackOverflow I've been trying to code (in R) a way to convert gene accession numbers to gene names (from RNAseq data). I've looked at all the related ...
Equinox's user avatar
  • 129
3 votes
2 answers
2k views

Find rsIDs for GRCh37 SNPs and rsIDs for GRCh38 SNPs and compare for overlap

I have a long list of variant IDs that I generated as a result of research done one GRCh37 genomes (e.g. 13_28025615_G_C_b37). I want to get their rsIDs and compare ...
CelineDion's user avatar
2 votes
1 answer
105 views

Discordance of Gene Ontology data between Mouse Genome Informatics and Ensembl sources

In my first approach to the use of Gene Ontology, I have found a discordance if we consult either Mouse Genome Informatics (MGI) or Ensembl for these data. Concretely, for the mouse genes Zic1 (NCBI ...
Faustino's user avatar
  • 123
1 vote
3 answers
190 views

How to obtain amino acid context at a given position

I'm trying to find the amino acid context around a particular position in a protein (5 aa amino acid window on each side). I used to have some code that works and then biomaRt stopped working. I ...
Will Gibson's user avatar
3 votes
1 answer
178 views

different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
gabt's user avatar
  • 348
7 votes
2 answers
38k views

Converting Gene Symbol to Ensembl ID in R

I'm trying to convert ~20,000 different human gene symbols to ensembl IDs. I've been trying to use biomaRt to do this, but continue getting the following error ...
Mea R.'s user avatar
  • 71
1 vote
1 answer
44 views

Where can I find the DNA sequence of the C. elegans rRNA cluster?

Where can I find the DNA sequence of the C. elegans rRNA cluster? Ideally, I would be able to do it using the command-line. I've tried using NCBI but the results are unsatisfactory. I am interested ...
Biomagician's user avatar
  • 2,459
1 vote
0 answers
147 views

Error in checkDataset, The given dataset: mmusculus_gene_ensembl , is not valid

I was perfectly using bioMart, but it gave an error, I went ahead trying to follow the following thread. And there were some issues with ...
Nikita Vlasenko's user avatar
3 votes
1 answer
231 views

BioMart Ensembl id imperfect retrieval

I have a list of gene symbols: ...
Nikita Vlasenko's user avatar
2 votes
1 answer
142 views

Off-by-one error when mapping Ensembl IDs to gene symbols

I have a matrix with ensemblIds which I am trying to convert to gene symbols using BioMart. Some of the ...
Nikita Vlasenko's user avatar
2 votes
1 answer
537 views

BioMart does not return a result

I am supplying to BioMart 81 ensemblIDs, but getting 80 ...
Nikita Vlasenko's user avatar
3 votes
1 answer
47 views

BioMart returns one more item

I am supplying 30 ensembl ids into BioMart, but somehow it returns 31 result. What is going wrong here? Here you can see the code: ...
Nikita Vlasenko's user avatar
4 votes
1 answer
144 views

Retrieval of genomic position by using biomaRt package

I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files). I'm looking for the genomic ...
Adrian Smith's user avatar
1 vote
0 answers
304 views

Cannot connect to BioMart webservice in R script, how to troubleshoot connection?

I'm attempting to query from BioMart in R using the biomaRt package with a script I've used many times before. I connect to the service with this line of code: ...
J0HN_TIT0R's user avatar
4 votes
1 answer
146 views

Counting the number of paralogues for mouse genes gives me the wrong frequency in R

I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. ...
Jack Dean's user avatar
5 votes
2 answers
648 views

BiomaRt error: Error in martCheck

I am experiencing an error while using getSequence() in biomaRt. The code is given below: ...
Learner's user avatar
  • 51
8 votes
2 answers
11k views

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart. I tried to get a kind of conversion table for all human genes. ...
floatingpurr's user avatar
5 votes
2 answers
7k views

Ensembl id to GeneSymbol with biomart

I have 3224 Ensembl id's as rownames in a dataframe "G". To convert Ensembl ids into Genesymbols I used biomart like following. ...
stack_learner's user avatar
3 votes
2 answers
272 views

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

Note: this question has also been asked on BioStars I am getting peptides using biomaRt library in R for the gene 'BRCA1'. 27 different aminoacid sequences are returned, and 12 of those have an ...
user5054's user avatar
  • 305
7 votes
1 answer
1k views

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I ...
J0HN_TIT0R's user avatar
7 votes
1 answer
497 views

Get RefSeq accession numbers with versions

Google searching for NM_002084 gives the following result: NM_002084.4 This, I assume, is the latest version v4, hence the .4 suffix. Searching for previous ...
zx8754's user avatar
  • 1,042
23 votes
4 answers
15k views

What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)

When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download? You have a combination of choices. First part options: ...
story's user avatar
  • 1,573
8 votes
3 answers
654 views

probeset to probeset mappings between Affymetrix arrays

I am interested in identifying mappings between different types of Affymetrix arrays. I am aware that mappings between gene and probeset can be extracted using Ensembl's Biomart database. ...
Prradep's user avatar
  • 410