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TCR reconstruction from Single Cell 3′ RNA-seq

Posted By: frank9, on Oct 20, 2018 at 8:30 PM

Hello, 10X ers,

 

Can I reconstruct the TCR sequences from Single Cell 3′ Library? I noticed 10X has another solution (Chromium Single Cell V(D)J Enrichment Kit), but we have not tried this product. By the way, is tracer (Stubbington, M. J. T., Lönnberg, T., Proserpio, V., Clare, S., Speak, A. O., Dougan, G., & Teichmann, S. 2016. T cell fate and clonality inference from single-cell transcriptomes. Nature Methods. http://doi.org/10.1038/nmeth.3800) suitable to perform such analysis?

 

Yours,

Frank

2 Replies

Re: TCR reconstruction from Single Cell 3′ RNA-seq

Posted By: rachanajain, on Oct 22, 2018 at 5:50 PM

Hi Frank,

 

We do not recommend using 3' solution for assembling full length TCR chains. You might not be able to assemble full length contigs for majority of your data.

 

If however, you have the data already, you could try using Tracer. We cannot guarantee how successful you will be since we have not valided this approach. Note that if you are using Tracer, you will need to tease out the fastqs for each cell-barcode  and feed then separately to Tracer for each cell.

 

This forum discussion might help: https://b-t.cr/t/b-tracer-on-10xgenomics-data/611

 

Thanks !

-Rachana

Re: TCR reconstruction from Single Cell 3′ RNA-seq

Posted By: frank9, on Nov 5, 2018 at 6:12 PM

Thanks Rachana, I have tried Tracer. Just as you mentioned, many cells do not have full-length contig.