Differential abundance analysis for bulk TCR-seq data

Question

[pm2012]

Hello Experts,

I am currently analyzing bulk TCR-seq data where we are looking at changes in TCR repertoire based on a treatment. I would like to identify sequences that show statistically significant differential abundance across conditions. As there are no specific tools for doing this type of analysis, I am wondering what would be the best way to go about this.

I came across the following paper, which uses modified version of DESEQ for determining differential abundance.

https://stm.sciencemag.org/content/6/238/238ra70

I have also looked at couple of other papers, which use Fisher's exact test along with multiple testing correction.

As my samples do not have replicates, I am wondering what would be the best way to go about this. I am not a statistician so any advice there would be highly appreciated.

[GenoMax]

Are these patient samples? If yes then you can't do much about replicates. Follow the protocol published for similar samples.

[pm2012]

Hi GenoMax Yes.

Answer 1

[swbarnes2]

It's not clear to me that you can do anything with statistical rigor without replicates.