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 ...
- 19.6k
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):
...
- 4,693
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 ...
- 9,662
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:
...
- 1,749
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 ...
- 6,485
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:
...
- 4,693
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 ...
- 1,749
8
votes
7
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.
- 3,301
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
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. ...
- 19.6k
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 ...
- 4,845
6
votes
Accepted
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 ...
- 1,749
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:
...
- 3,571
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:
<...
- 1,749
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 ...
- 3,928
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 ...
- 19.6k
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 ...
- 1,882
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.
- 1,262
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.
- 1,573
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.
- 31
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....
- 151
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.
- 1,749
Only top scored, non community-wiki answers of a minimum length are eligible