B/Tracer on 10Xgenomics data


Did anybody already tried to retrieve BCR/TCR information from the 10Xgenomics 3’ gene expression data using Tracer and Bracer? How well does it work?


We’ve seen some evidence that you might be able to reconstruct sequences in some cells although it’s definitely not optimal and hasn’t been validated on 10x data. You also have to demultiplex the sequencing output into individual FASTA files for each cell for input.
We heard from the authors of the TraCeR and BraCeR papers that they didn’t try this when developing the tools because they didn’t expect it work. Of course, it is hard to say whether the reconstructed sequences are genuine or not. They’re typically not full-length either although sufficient for annotation