Questions tagged [ensembl]

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31 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 ...
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1answer
69 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 ...
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0answers
36 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 ...
2
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2answers
56 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 ...
2
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2answers
45 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: ...
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0answers
28 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 significantly different. ...
0
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1answer
62 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 ...
0
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2answers
84 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....
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1answer
50 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 ...
1
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1answer
28 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 ...
2
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1answer
83 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 ...
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3answers
666 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?
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1answer
51 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 ...
3
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4answers
172 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 ...
1
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1answer
525 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
3
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2answers
12k 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
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1answer
67 views

Error while performing “lift-over” of genomic coordinates between two species using Ensembl Compara API

I'm trying to convert coordinates between the reference mouse genome and CAST/EiJ mice strain. Since Ensebml already has alignment available in the browser, I decided to use Ensembl perl API to lift ...
0
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1answer
154 views

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

I have many scRNAseq datasets saved as hdf5 files, and when I open them keys sometimes are confused, so I need a way of ...
5
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4answers
1k 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 ...
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2answers
701 views

Python API for working with ENSEMBL genomes

Dear bioinformaticians, I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is ...
2
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1answer
50 views

Comparing two files with overlapping regions and get their associated information

I have two file that have overlapping regions. One file has chromosomes, position, CNV data and samples.Other file has chromosomes, positions and ensemble ids of genes. Here is some lines of two ...
3
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1answer
33 views

Is there a way to tell which chromosome a gene is on, by looking at the “Chromosome/scaffold name”

I recently got a data set, from which I need to figure out which chromosome a gene is from, but the head of the data reads like: ...
3
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1answer
78 views

tximport txidcol and geneidcol selecting wrong column

I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, ...
3
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1answer
141 views

How to filter Ensembl cDNA and ncRNA FASTA files by primary assembly?

I'm currently performing differential expression analysis using alignment-free quantification using Kallisto. To do this, I need to create a Kallisto index using Ensembl's cDNA and ncRNA annotations ...
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0answers
177 views

Cannot connect to BioMart webservice in R script, how to troubleshoot connection?

I'm attempting to query from BioMart in R using the biomaRt package with a script I've used many times before. I connect to the service with this line of code: ...
2
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1answer
334 views

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

I am interested in downloading all the files at: ftp://ftp.ensembl.org/pub/release-91/embl/bos_taurus/ I know how to download a single file from that page using wget (Unix) or download.file() (R) ...
4
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1answer
134 views

Counting the number of paralogues for mouse genes gives me the wrong frequency in R

I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. ...
2
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2answers
205 views

Is there any R package for biodbnet?

I want to convert Ensembl ids to Gene_symbols. I used biomaRt package but all Ensembl ids are not seen in the results. Examples of problematic IDs are: ENSG00000255414, ENSG00000274358, ...
5
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2answers
6k 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. ...
2
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1answer
118 views

Is there a way to retrieve ENSEMBL IDs from a search query?

I would like to be able to batch download FASTA files from ENSEMBL. I normally would use the API to download them from the ENSEMBL gene IDs. However, the IDs aren't ones I know, only ones I would get ...
7
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1answer
775 views

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I ...
19
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4answers
7k 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: ...
9
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3answers
496 views

probeset to probeset mappings between Affymetrix arrays

I am interested in identifying mappings between different types of Affymetrix arrays. I am aware that mappings between gene and probeset can be extracted using Ensembl's Biomart database. ...
40
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5answers
7k 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)...