Hot answers tagged

24 votes
Accepted

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

To add to rightskewed answer: While it is true that: Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl), the annotation (GTF) files are quite ...
user avatar
  • 504
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 ...
user avatar
  • 19.2k
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): ...
user avatar
  • 4,622
12 votes

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

Ensembl vs Gencode https://www.gencodegenes.org/faq.html The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical ...
user avatar
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 ...
user avatar
  • 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 ...
user avatar
  • 5,794
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: ...
user avatar
  • 4,622
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 ...
user avatar
  • 191
6 votes

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

To add practical advice to what others have said: In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off. Ensembl aims ...
user avatar
  • 3,221
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. ...
user avatar
  • 19.2k
6 votes

Python API for working with ENSEMBL genomes

Now there's another option, the ensembl_rest module, a thin wrapper around the Ensembl REST API to simplify its usage and make it more pythonic. You can find the ...
user avatar
  • 61
6 votes

Converting Gene Symbol to Ensembl ID in R

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

How to download the whole directory of an ensembl FTP page?

You can use the mirroring function of wget: wget -m ftp://ftp.ensembl.org/pub/release-91/embl/bos_taurus/
user avatar
5 votes

Why the gene symbol aliases have significantly different sequences?

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 ...
user avatar
4 votes
Accepted

Is there any R package for biodbnet?

I couldn't find a package neither in Github nor in Bioconductor. Neither could I find any paper about a package linking to bioDBnet. So I don't believe there is any (R) package at the moment which ...
user avatar
  • 4,622
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 ...
user avatar
  • 3,527
4 votes
Accepted

Python API for working with ENSEMBL genomes

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

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

The three # are used for splitting group of features that belong together, e.g. a transcript and it's exons. Sometimes you see with a blank line instead of the <...
user avatar
  • 1,332
4 votes
Accepted

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

There are some good answers so far, but I don't think any of them fully communicate the significance of the ### directive. The GFF3 specification states: This ...
user avatar
4 votes
Accepted

Matching these matrices in R

Since they share the ensembl_ID column, you can merge them, then assign the symbol column to the rownames, then delete the symbol column. something like: ...
user avatar
  • 1,672
4 votes
Accepted

CDS length for each human gene

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for ...
user avatar
  • 8,161
4 votes
Accepted

Getting species from ensembl sequence id

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.
user avatar
4 votes
Accepted

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

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 ...
user avatar
4 votes

Ensembl protein identifiers from different assemblies

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 ...
user avatar
4 votes
Accepted

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

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 ...
user avatar
4 votes

How to identify which isoforms of a gene are actually expressed in my data?

Tools like kallisto or salmon can perform a process call pseudo-alignment that matches reads from RNA-seq data to transcript isoforms present in a reference genome. You can then look at the output of ...
user avatar
  • 1,192
3 votes

Finding gene length using ensembl ID

You could also do this in R with the GenomicFeatures library. ...
user avatar
  • 1,498
3 votes
Accepted

Finding gene length using ensembl ID

If you really just want the start and end positions of all genes in a list of genes from Homo_sapiens.GRCh38.93.gtf.gz, you could do this in awk. For example, if ...
user avatar
  • 8,161
3 votes
Accepted

Comparing two files with overlapping regions and get their associated information

You can use bedtools intersect and cut the results: ...
user avatar
  • 19.2k
3 votes

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

As others have stated, those are just there to separate the entries for easier parsing. They enable you to do nifty tricks like: ...
user avatar
  • 8,161

Only top scored, non community-wiki answers of a minimum length are eligible