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1 answer
50 views

Differences between Gencode GTF and Ensembl GTF files

I recently switched from RSEM to Salmon for RNAseq data processing. I started in the Ensembl world and wrote a lot of code around their GTF file (for filtering biotypes/normalization lists etc, http://...
1 vote
2 answers
535 views

Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?

I have single cell data which I want to annotate with the seurat package, so I ran this code in R: ...
0 votes
1 answer
206 views

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 : ...
1 vote
2 answers
35 views

How to download the same 18S rRNA gene region for multiple species?

I need 18S rRNA gene sequences for a wide variety of eukaryotic species. I know that Ensembl has this gene sequence, but I don't understand what is the correct protocol to download the sequences. I ...
48 votes
6 answers
15k views

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

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...
0 votes
1 answer
37 views

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 ...
1 vote
1 answer
47 views

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 ...
2 votes
1 answer
44 views

Dog (Canis lupus familiaris) MT gene annotations

I have an RNA-Seq and scRNA-Seq dataset from dog samples and pseudo-aligned them to the dog reference transcriptome (Ensembl release 109). When filtering for mitochondrial gene percentage in scRNA-Seq ...
3 votes
1 answer
76 views

What is the best way to acquire protein isoform sequence alignment?

[Update] Thanks @terdon. To clarify my question: I have a bunch of protein isoforms sequences (produced by the transcripts in the figure) and I want to align protein products (e.g., proteins produced ...
0 votes
1 answer
73 views

VEP annotation INFO field Ensembl IDs and locations

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is ...
0 votes
1 answer
26 views

Current 'most comprehensive' whole genome alignment resource for human?

I found the human genome alignment sets here: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html but they doesn't include, for example, ancient human genomes, e.g. those here: ...
1 vote
0 answers
29 views

How to make a POST "vep/:species/region" request that is able to accomodate multiple alternate alleles for a single variant?

There is an R code example on Ensembl's website on how to execute a POST "vep/:species/region" request for variants that only have one alternate allele. The part that holds the variant data ...
3 votes
1 answer
37 views

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?

I need to match the external gene names of a table I have called (which has 1,000,000 entries) with their respective ensemble gene IDs. Here's a small subset of df: ...
23 votes
4 answers
15k views

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: ...
3 votes
0 answers
78 views

Different human reference genomes from NCBI and ENSEMBL, and variant annotation with Variant Effect Predictor (VEP)

Background: I have been working on a human variant calling pipeline, from whole exome reads to variant annotation. For variant annotation I used the Variant Effect predictor (VEP), which is Ensembl ...
1 vote
1 answer
537 views

Error of duplicated rownames although there are no duplicates

I have a data frame that I want to switch its row names from EnsembleID (GENEID) to gene symbol (SYMBOL). When I try to switch, I get this error: ...
3 votes
1 answer
99 views

Exon number between GTF file and ENSEMBL site does not match

Based on the ENSEMBL GTF file, I counted the number of exons per gene as follows: ...
5 votes
2 answers
503 views

Error installing VEP on mac

I have tried multiple different ways to get Ensemble's Variant Effect Predictor (VEP) to properly install on my mac, but I keep getting same error. ...
1 vote
1 answer
299 views

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: ...
1 vote
1 answer
250 views

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 ...
1 vote
1 answer
99 views

Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF

I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this: ...
2 votes
2 answers
606 views

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

I am new to bioinformatics and have been assigned the task of discovering which isoforms of a certain protein-coding gene are present in the RNA-seq data that I have. There are several isoforms of ...
0 votes
0 answers
406 views

How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?

I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. ...
2 votes
1 answer
44 views

It is possible to have a UniProt protein entry that does not have any genomic coordinates, because lacks of an Ensembl link?

I have a list of UniProt codes and I am trying to fetch the genomic coordinates through the API from programmatic access to UniProtKB (https://www.ebi.ac.uk/proteins/api/doc/). Moreover, I read that ...
0 votes
1 answer
363 views

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

I have downloaded a dataset containing RNA-Seq RPKM (reads per kilobase per million) values for 52376 genes (in humans). To find RPKM values for the gene KIR2DL2 in the dataset, I have to search for ...
0 votes
1 answer
31 views

Synteny test and tools to use for mammalian organisms?

I am trying to do a synteny test for MHC genes in human and another mammalian organism For this reason, I need to download all paralogs of rabbits from humans and then construct position the ...
1 vote
1 answer
342 views

Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
0 votes
0 answers
39 views

Identifying Variant Conservation Across Species

I've got gene sequences of mouse genes. Each sequence contains variants from the reference genome. I need to find out whether these SNPs/variations are in functionally significant regions (i.e. exons)....
1 vote
1 answer
1k views

Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids

I want to use a file available on a database called DepMap (https://depmap.org/portal/download/). This file called ...
2 votes
1 answer
420 views

How do I create a VCF file of all known pathogenic mutations in a gene of interest?

I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same ...
0 votes
0 answers
75 views

Best resource to link a gene/protein to a druggability score?

Could I ask, is anyone familiar with the Drugebility score provided by Chembl? I wanted to add a druggability score to a set of human targets, to understand the likelihood that they are druggable. I ...
7 votes
2 answers
39k views

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 ...
2 votes
1 answer
87 views

Splice variant analysis with ensembl genome/annotation/rna. Which files do I use?

I am running splice variant analysis. I wanted to use NCBI genome but the program works better with ensembl. I am a bit confused on primary vs. top level to use as my reference genome. I also do not ...
1 vote
2 answers
125 views

Why the gene symbol aliases have significantly different sequences?

"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are ...
0 votes
1 answer
50 views

Getting all variants in a region from ensembl

I want to get all the variants (SNPs) in a given region of the human genome. Is there a way on how to do this with the ensembl-API? It should be a representation similar to this: There I added dbSNP ...
1 vote
1 answer
42 views

Using txt file to query Ensembl API

I am trying to use an external file with a list of gene names to query the ENSEMBL IDs using the perl API. This script works: ...
0 votes
1 answer
181 views

getGeneLengthAndGCContent in EDASeq complains about "Ensemble gene ID"

I am trying to use the getGeneLengthAndGCContent function from the EDASeq library to retrieve gene lengths for c. elegans. I ...
1 vote
2 answers
813 views

What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100

3 solutions that I had to unfortunately rule out. Potential solution #1 As far as I know, the conventional way is to do this is by using CCDS ids (e.g. using biomart). However, the issue is that, as I ...
1 vote
0 answers
226 views

10x Single-cell RNA-Seq - Updating gene symbol with latest ensembl release - Ensembl IDs missing

I am trying to update the gene symbols provided by the 10x human precompiled reference (2020-A), using the mapping Ensembl ID to gene symbol provided in release 102. However, I found out that 56 of ...
1 vote
2 answers
537 views

Check if a string is ensembl gene id or not in python

I have many scRNAseq datasets saved as hdf5 files (hierarchical data format*), and when I open them keys sometimes are confused, ...
1 vote
0 answers
154 views

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 ...
0 votes
0 answers
51 views

Finding a gene of similar length

I would like to find a few genes that are similar in length to a gene of interest, and by that I mean the total length of a canonical transcript including introns. This is proving to be surprisingly ...
1 vote
0 answers
285 views

How are the scores of GeneSplicer, MaxEntScan and SpliceRegion interpreted from VEP annotations?

I am using VEP from Ensembl to annotate my VCF files with the extra plugins of GeneSplicer, MaxEntScan and SpliceRegion. However, I don't fully understand the output of these scores. I know that they ...
5 votes
2 answers
7k views

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. ...
0 votes
1 answer
2k views

How to map gene names to ensembl Ids in R

I am trying to convert a list of gene names into Ensembl IDs but I'm having a bit of trouble. I've tried using the EnsDb.Hsapiens.v86 package but I always get LRG-ID values returned as well, even ...
3 votes
4 answers
275 views

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

I downloaded the annotation of the C. elegans genome in GFF3 format from Ensembl. I typed the following command, hoping to get the header of the file (lines starting with ...
2 votes
2 answers
52 views

select unique names while removing the duplicates from a column

I have a file with Ensembl gene and Transcript IDs : I want to retain only the first entires from both the column so that the output looks like this: ...
6 votes
4 answers
5k views

Finding gene length using ensembl ID

I want to find the length of a list of genes, of Homo sapiens, that is reported in the GEO database. I have gathered the ensembl id's of those genes. I understand this information can be parsed from ...
2 votes
2 answers
339 views

How to download multiple proteomes at once?

I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best ...
0 votes
1 answer
430 views

Ensembl protein identifiers from different assemblies

In order to obtain orthologs for human genes, I am working with InParanoid version 7.0. This version of the database uses Ensembl Protein Identifiers (ENSP) from ENSEMBL version v54, which is based on ...