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
Human TRB AIRR-Seq datasets added
VDJbase now has a dataset based on TRB AIRR-Seq repertoires. This data is analysed in Omer et al., 2022, in which we demonstrate that methods developed for the inference of allelic variants in the B cell repertoire can also be applied to the T cell repertoire. Many T cell studies sequence just a short fraction… Continue reading Human TRB AIRR-Seq datasets added
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
Human IGK and IGL AIRR-Seq datasets added
This summer we added human IGK and IGL AIRR-Seq datasets to VDJbase. These comprise those of the IGH studies which also provided light chain sequencing. You can find details of the studies on the Explore Data page – select the required dataset at the top of the page to view statistics.
Allele Review Extended
OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly.
Rhesus Macaque Genomic data added
VDJbase now includes annotations of two sequences of the Rhesus Macaque IGH locus. The first is from the current rheMac10 Reference Assembly, and the second (which is presented as 13 contigs rather than a single assembly) is from a study by Cirelli et al. Annotation was conducted using Digger. Gene names used follow those from… Continue reading Rhesus Macaque Genomic data added