Hi, I have an RNAseq data from TCR alpha and bed chain single cell sequencing which I am trying to analyze. I looked at the post TCR sequence analysis and also read the Mark Davis paper and the protocol, which I thought would be appropriate to follow. But I cannot either find the dataset from the Mark Davis paper not the tool they used (vdjfasta). I was writing to ask what is the latest tool that would be appropriate for assembling the reads and getting a summary the TCR clones from my dataset. Thanks, - Pankaj
Software for T/B-cell receptor repertoire analysis using non-amplicon samples:
P.S. Check out T cell fate and clonality inference from single-cell transcriptomes (Nature Methods 2016) that describes your case.
Hi there! I have a brief technical question to this paper - for the 3rd PCR: it sounds like, according to the methods part, that one needs to add the 2 Illumina paired-end primers to the actual 3rd PCR? In addition to the Barcode primers, is that correct?
I usually submit these with the actual sample to the core. Also, don't we also need an index primer?
Would appreciate your help that I can get to where you already are :) Thanks