Creating an OGRDB Submission

Pre-Requisites Before submitting inferred sequences with OGRDB, you should have run OGRDBstats on each repertoire, and created select sets and sequence definitions in NCBI or ENA: otherwise, please follow steps 1-3 in the overall submission process before continuing. You should therefore have: OGRDBstats output (pdf and csv) for each repertoire from which inferences have been… Continue reading Creating an OGRDB Submission

Categorised as VDJbase

IARC Submission Guide Updated

We welcome submissions of previously undocumented alleles of human receptor genes. The Submission Guide explains the process, which involves deposition of sequences and sequence sets in NIH or ENA repositories. Your submission will be reviewed by AIRR‘s Inferred Allele Review Committee, and, if there is sufficient evidence, the sequence will be published on this site… Continue reading IARC Submission Guide Updated

Categorised as OGRDB_News

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