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 ...
- 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 ...
- 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
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 ...
- 991
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
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
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 ...
- 3,301
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
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 ...
- 61
6
votes
Converting Gene Symbol to Ensembl ID in R
I tried several R packages (mygene, org.Hs.eg.db, biomaRt, ...
- 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/
- 218
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 ...
- 1,749
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 ...
- 4,693
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
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.
- 1,749
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 <...
- 1,342
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 ...
- 5,060
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:
...
- 1,882
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 ...
- 9,662
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.
- 1,749
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 ...
- 1,749
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 ...
- 1,749
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 ...
- 1,749
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 ...
- 1,374
4
votes
Accepted
Error of duplicated rownames although there are no duplicates
I found an answer shortly after posting this question:
...
- 169
4
votes
Why does the subset of rows that match a condition added by the rows that don't match a condition not add up to the total number of rows?
From a brief glance, the gap is not in your code but in your expectations. You're operating based on an assumption of 1:1 mapping between ENSG IDs and HGNC symbols (your ...
- 2,086
3
votes
Finding gene length using ensembl ID
You could also do this in R with the GenomicFeatures library.
...
- 1,573
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 ...
- 9,662
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