Questions tagged [biomart]
The biomart tag has no usage guidance.
34
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annotate ChIP-Seq peaks
I'm attempting to annotate several peaks with various approximations. Nevertheless, the expected results are not achieved.
T_S_1 is a Granges object which the ...
- 179
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1
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63
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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 ...
- 69
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38
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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 ...
- 29
3
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1
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54
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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.
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- 179
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355
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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:
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1
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318
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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 ...
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1
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166
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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
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- 27
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1
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230
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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 :
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570
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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 ...
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166
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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 ...
- 695
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316
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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.
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- 159
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371
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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 ...
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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 ...
- 277
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1
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110
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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 ...
- 133
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3
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194
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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 ...
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178
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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 ...
- 348
7
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2
answers
40k
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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
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46
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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 ...
- 2,479
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152
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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 ...
- 2,578
3
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1
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234
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2
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1
answer
148
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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 ...
- 2,578
2
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1
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567
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3
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1
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51
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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:
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4
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1
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147
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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 ...
- 357
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0
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313
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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:
...
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4
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147
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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. ...
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660
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BiomaRt error: Error in martCheck
I am experiencing an error while using getSequence() in biomaRt.
The code is given below:
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2
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11k
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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. ...
- 315
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7k
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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.
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- 1,272
3
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2
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279
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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 ...
- 305
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1
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1k
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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 ...
- 541
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506
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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 ...
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24
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4
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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:
...
- 1,603
9
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3
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687
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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.
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