How to get annoted immunoglobulin loci in Ensembl · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

How to get annoted immunoglobulin loci in Ensembl

I want to do some research in noncoding region, and I am following a paper, which avoid immune system-coupled somatic hypermutation (SHM) by removing annoted immunoglobulin (Ensembl). I tried to find them in gtf file by using keyword, failed. I surfed on Ensembl and search it, a lot of text information returned. (search result) How can I get a summary file contains gene name or gene location of all immunoglobulin loci?

Thanks.

genome gene

• 1,501 views • link

written 9.3 years ago by wangshx •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

mRNA counts
written 3.3 years ago by t.ru •

Hi, I have mRNA count files with contains IDs like ENSG00000200494 (https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000200494;r=20:16670641-16670742;t=ENST00000363624). The ensembl website shows as noncoding part of RNAs. However, the file is …
Domain coordinates from InterPro to Ensembl transcripts
written 6.8 years ago by svet.sidorov

Hello! Is it possible to obtain InterPro coordinates of a protein domain in human alternative protein-coding transcripts from Ensembl? For example, for [TFAP2A gene][1], Ensembl …
Different Ensembl Ids point to the same gene symbol.
written 7.1 years ago by elefth.pavlos •

Hi all, I have a matrix with RNA-seq counts of reads. Ensemble gene IDs in rows, samples in columns. I want to check for differential …
Ensembl ID found on the site but not in downloaded flat file
written 7.4 years ago by Chat-ra •

Hello everyone! I’ve downloaded several Ensembl file (the entrez and uniprot ones) found here: http://ftp.ensembl.org/pub/release-95/tsv/homo_sapiens/ While working I’ve encountered an issue. Some of the Ensembl …
How to understand somatic mutation of ICGC data
written 9.2 years ago by wangshx •

I am new to process somatic mutation by ICGC data. In ` simple_somatic_mutation.aggregated.vcf.gz`(https://dcc.icgc.org/releases/current/Summary), I got `vcf` format file. Every `Mutation ID` in the data annotated …
Convert Gene location from one human genome build to another
written 9.2 years ago by akij

I have some genes list and I need to find the chromosome position of those genes. I found 2 web service for this, [ncbi][1] and …
Retrieve Ensembl webpage link
written 10.3 years ago by ignasi_11 •

Does anyone know if it is possible to retrieve the ensembl gene information webpage given an Ensembl ID? All the stable ids for different species …
Ensembl: Map between different assemblies of one ensembl release
written 11.2 years ago by hendrik •

There are ensembl gene ids which are mapped not on the primary assembly but on an alternative sequence. On the ensembl website (http://www.ensembl.org) it is …
Retrieving only ENST ids linked to an ENSG ids using the Ensembl REST API
written 12.1 years ago by Fred Fleche

<p>Hi,</p> <p>Let's say that I want to programmatically retrieve in json format the 4 Ensembl transcripts IDs that are linked to the Ensembl gene ENSG00000133703 …
misc_RNA in Ensembl
written 12.2 years ago by Martombo

Do you know which are the criteria used to classify a gene as `misc_RNA` by Ensembl? I couldn't find an answer on [the Ensembl page …