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13 votes

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

There's rarely a good reason to use a hard-masked genome (sometimes for blast, but that's it). For that reason, we use soft-masked genomes, which only have the benefit of showing roughly where repeats ...
  • 19.3k
12 votes

Converting Gene Symbol to Ensembl ID in R

You can use the standard annotation package for humans (you can also use biomaRt, but it can be more confusing, see below): ...
  • 4,622
9 votes
Accepted

BioMart does not return a result

Whenever you are wondering about things like this, just look up the identifier on the Ensembl web page. If you look up ENSMUSG00000083840, you will see: This ...
  • 8,525
9 votes

BiomaRt error: Error in martCheck

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: ...
9 votes
Accepted

probeset to probeset mappings between Affymetrix arrays

If your question is: can probeset IDs from different platforms be mapped to one another in a similar way as mapping probesets to genes, then the answer is: Yes. BioMart allows you to map almost ...
  • 646
9 votes
Accepted

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

Generally, you should use the soft-masked or unmasked primary assembly. Cross-species whole-genome aligners, especially older ones, do need to know soft-masked regions; otherwise they can be ...
  • 6,052
8 votes

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

You need to specify the number without the version. Instead of "ENSMUST00000178862.1" just "ENSMUST00000178862": You can do this with one more line: ...
  • 4,622
8 votes
Accepted

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

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 ...
7 votes

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Conversion using R: ...
  • 2,594
7 votes

probeset to probeset mappings between Affymetrix arrays

Instead of biomaRt, it is also possible to use the mapping databases built into Bioconductor itself, and map from probe to gene, and then from gene to probe in the second. Some R code to convert ...
  • 191
6 votes
Accepted

Get RefSeq accession numbers with versions

I don't believe this is possible using biomaRt, nor using AnnotationHub. I have two suggestions, neither of them very ...
  • 646
6 votes
Accepted

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID.
  • 3,241
6 votes

Ensembl id to GeneSymbol with biomart

It looks like you were using an old annotation. The problematic IDs you posted existed in the GRCh37 annotations, but don't in the most recent GRCh38 annotation. For that reason they were excluded. ...
  • 19.3k
6 votes

Converting Gene Symbol to Ensembl ID in R

I tried several R packages (mygene, org.Hs.eg.db, biomaRt, ...
  • 161
6 votes
Accepted

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

There’s no 1:1 mapping between the IDs of different database schemas. As a consequence, some Ensembl gene IDs map to multiple MGI symbols, or to none (and vice versa). Therefore, you can’t assume ...
6 votes
Accepted

BioMart returns one more item

If you print G_list, you'll see this half way down: ...
  • 1,806
4 votes

Retrieval of genomic position by using biomaRt package

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 ...
4 votes

BioMart Ensembl id imperfect retrieval

The genes that are missed are probably not official mgi symbols. You might wanna look them up at mgi: ...
  • 3,551
4 votes
Accepted

different results coming from biomart online and biomaRt R library

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: <...
4 votes

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

Which tools/aligners take into account softmasked repeat regions? If you're doing whole genome - whole genome alignment (rather than read alignment) then using the softmasked genome is definitely ...
  • 3,587
4 votes

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

If you look at the original data at Ensembl you'll notice that most of these are labeled "CDS 3' incomplete" and have a TSL (transcript support level) of 1, which is as low as it goes. It seems likely ...
  • 19.3k
3 votes
Accepted

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

it's not clear to me that it would support both versions of genome builds. You can specify what version of the database you are querying. I'd start with biomart on the ensembl website, see if you ...
  • 1,782
2 votes
Accepted

Ensembl id to GeneSymbol with biomart

I used gProfileR where there are no problematic IDs with that. It converted ENSEMBL IDs to Gene_symbols and made my work easier with GO analysis too. There is an R package and also API.
2 votes

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

TOPLEVEL These files contains all sequence regions flagged as toplevel in an Ensembl schema. This includes chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions. E....
2 votes

probeset to probeset mappings between Affymetrix arrays

Other answers explain why there might not be one to one mapping between the probes. The AbsID database does conversion based on mapping the probe sequences to a genome build, and then determines ...
  • 191
2 votes

How to obtain amino acid context at a given position

You could also save your "biomart_query_result" object after the first time it is generated. Then you can re-use it without having to depend on the biomaRt API functionality.
  • 1,568
2 votes

How to obtain amino acid context at a given position

It turned out that I needed to reinstall OSX to upgrade my R version and biomaRt install.
2 votes

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

rsIDs change with the dbSNP builds, not with the reference genome builds. rsIDs do not depend on a reference genome. They point to a specified locus regardless of the differences in genomic assemblies....
1 vote

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

Short answer, we get our annotations from GOA, which has the three listed. We're in touch with GOA to see why they differ from MGI.

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