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10x Genomics
Chromium Single Cell Immune Profiling

Prebuilt References

This page provides some details about the prebuilt human and mouse reference sequences (downloadable here). These reference were created from V(D)J genes in Ensembl build 94, using both gtf and gff3 files, which provide slightly different information. The process is mechanical, and supplemented by manual edits, which we describe in detail here. There are two cases where we created unofficial gene names, and these should ultimately be replaced by official names.

One consequence of these changes is that all V gene sequences now begin with a start codon ATG. (This lies in the leader sequence coding for a signal peptide that is cleaved off.)

For the prebuilt references, pseudogenes are excluded, except where we think the pseudogene labeling is incorrect, for specific instances described below.

Human V(D)J gene edits

Mouse V(D)J gene edits