how to check whether there is TCR alpha alpha in the scTCRseq.

[synatkeamsk]

Hi Nick and team,

Hope you are well. I have a quick question. I recently had a quick discussion with one of our collaborators and she asked whether there is TCR alpha alpha in our sequencing data. I looked at my data frame of each sample (kindly review attach file), I saw only TRA and TRB. I am not sure is there is a quick way to check whether there is TCR alpha alpha in my dataset or they are only TCR alpha and beta using scRepertoire package.

Kind Regards,

synat

[ncborcherding]

Hey Synat,

If you are using the output of combineTCR() you can use the following code to isolate possible dual A T cells:

lapply(combined, function(x) {
  x$TRA.chains <- stringr::str_split(x$CTaa, "_", simplify = TRUE)[,1]
  dual.pos <- grep(";", x$TRA.chains)
  x[dual.pos,]
  
}) -> filtered.combined

Nick

[synatkeamsk]

Thanks, Nick for your code to filter out possible CTaa. Do you know which column (chain column?) that may possibly contains CTaa? I would like to manually check individual sample a bit to make sure whether I can see CTaa by eyes. So I can use code sth like df[df$chain == "CTaa", ] to check. Now I could not find CTaa somewhere in my dataframe. Sorry if the question is a bit naive and thank for your help.

Kind Regards,

Synat

[ncborcherding]

Hey Synat,

That code is for after you use combineTCR(). If you are looking at the filtered_contig_annotations file, you could use a dplyr approach to summarise the cells with more than 1 alpha chain:

df %>%
  filter(chain == "TRA") %>%
  group_by(barcode) %>%
  n()