The AIRR-C standard germline sets published in OGRDB use a new naming scheme: please see this poster for details. Because the format of these names may not be compatible with all current pipeline tools, we have released receptor-germline-tools: utilities that can convert to more compatible subgroup-identifier-allele form. We have also updated the FASTA files downloadable… Continue reading Tools for working with germline sets
Tag: howto
Introduction to OGRDB
Introduction to OGRDB In recent years it has become possible to sequence immune receptor repertoires (immunoglobulins and T cell receptors) at great depth. The accurate analysis of these repertoires requires a comprehensive understanding of the germline genes that give rise to the repertoire through V(D)J gene recombination. Even for well-studied species such as humans and… Continue reading Introduction to OGRDB
Genomic data in VDJbase
Genomic data is organised into ‘genomic sets’: typically a genomic set will contain data relating to a single locus of a species. At the moment, VDJbase holds genomic data for Rhesus Macaque but not for Human: when entering the Genomic pages, be sure to select Rhesus Macaque as the species at the top left hand… Continue reading Genomic data in VDJbase
Downloading data
Select the sample or allele data that you would like to download by using the filters, and press Download. For sample data, ‘csv’ will download a csv file with the information displayed on the Sample page, while ‘zip’ will download all files and reports for the selected samples. For alleles, ‘Gene information’ provides the information… Continue reading Downloading data
Analysing data
To analyse data using VDJbase’s built-in reports, first select the saimples you are interested in by using the filters, then go to the Reports page. This will display the analyses available for your selection. Note that many analyses will only run with a single dataset selected. If you do not set any filters, the analysis… Continue reading Analysing data
Searching for AIRR-Seq records
You can display multiple data sets for the same species where these are available: first select the species of interest, then check the datasets for that species that you wish to search. Usually these will correspond to individual loci. VDJbase uses an Excel-style approach to searching and browsing data: click on the little triangle to… Continue reading Searching for AIRR-Seq records
AIRR-Seq data: Allele Names
The Germline Genes page lists all alleles discovered in the data set(s). The Appearances column counts the number of individuals in which each allele is found. You can click on a number in the Appearances column to view a list of samples containing instances of the allele. Note that the number of samples may not… Continue reading AIRR-Seq data: Allele Names
AIRR-Seq data: Sample Names
VDJbase uses a structured name such as P1_I41_S1 to refer to each sample. The numbers following P, I and S are allocated serially by VDJbase. P indicates the project number. You can see a list of projects on the Explore Data page. I is followed by a number identifying the individual within that project, and… Continue reading AIRR-Seq data: Sample Names
Citing VDJbase
If you use VDJbase in your work, please cite our paper: Aviv Omer, Or Shemesh, Ayelet Peres, Pazit Polak, Adrian J Shepherd, Corey T Watson, Scott D Boyd, Andrew M Collins, William Lees, Gur Yaari, VDJbase: an adaptive immune receptor genotype and haplotype database, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D1051–D1056,… Continue reading Citing VDJbase