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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://...
Freek's user avatar
  • 573
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 ...
Mirk's user avatar
  • 33
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 ...
ToTheMoon's user avatar
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 ...
Alexandria Kouri's user avatar
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 ...
Dan Bolser's user avatar
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 ...
Jen Marylin's user avatar
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: ...
Rita Soares's user avatar
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 ...
Dandelion's user avatar
  • 353
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: ...
Dan Bolser's user avatar
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 ...
Derk's user avatar
  • 11
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: ...
Feynman's user avatar
  • 71
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 ...
Dandelion's user avatar
  • 353
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: ...
justinian482's user avatar
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. ...
Andrew's user avatar
  • 51
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: ...
An Ignorant Wanderer's user avatar
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 ...
An Ignorant Wanderer's user avatar
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: ...
justinian482's user avatar
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: ...
Programming Noob's user avatar
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 ...
Sawason's user avatar
  • 21
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. ...
Abhishek Pandey's user avatar
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 ...
ceno980's user avatar
  • 159
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 ...
mk894's user avatar
  • 105
1 vote
1 answer
342 views

Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
sakshiR's user avatar
  • 11
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)....
syrupflow's user avatar
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 ...
user345394's user avatar
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 ...
Giamma Fer's user avatar
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 ...
Slowat_Kela's user avatar
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 : ...
user1595929's user avatar
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 ...
Christa Frodella's user avatar
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 ...
Cowboy_Patrick's user avatar
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: ...
user45678789's user avatar
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 ...
user345394's user avatar
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 ...
Nereus's user avatar
  • 209
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 ...
gc5's user avatar
  • 1,813
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 ...
user345394's user avatar
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 ...
tacrolimus's user avatar
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 ...
An Ignorant Wanderer's user avatar
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 ...
Jack Henry's user avatar
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 ...
user324810's user avatar
  • 1,125
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 ...
Laura's user avatar
  • 937
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: ...
Amit's user avatar
  • 133
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 ...
Riq's user avatar
  • 35
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 ...
plat's user avatar
  • 1,042
0 votes
2 answers
1k views

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

I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl. However, for GRCh37, this option does not exists....
user324810's user avatar
  • 1,125
0 votes
1 answer
63 views

Where can I get ensembl Medaka genome for RNAseq

I am trying to map a RNA-seq dataset using ensembl genome for medaka fish. From here http://uswest.ensembl.org/Oryzias_latipes/Info/Index when I click on a ...
Mark's user avatar
  • 103
1 vote
1 answer
78 views

Getting species from ensembl sequence id

I have downloaded some orthologues from ensembl website in fasta format. The problem is that it uses the ensembl sequence id as name for the sequences. I want to know the species name or any other ...
juanjo75es's user avatar
2 votes
1 answer
108 views

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

In my first approach to the use of Gene Ontology, I have found a discordance if we consult either Mouse Genome Informatics (MGI) or Ensembl for these data. Concretely, for the mouse genes Zic1 (NCBI ...
Faustino's user avatar
  • 123
3 votes
3 answers
2k views

CDS length for each human gene

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?
solimanelefant's user avatar
0 votes
1 answer
98 views

Matching these matrices in R

I have two matrices; I want to convert the row names of first matrix to gene symbol from matched ensemble=gene symbol from second matrix ...
Zizogolu's user avatar
  • 2,160
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 ...
Biomagician's user avatar
  • 2,459