Issue with sequencing clustering with 10x paired BCR data

[meredithramba]

Hello,

I am trying to run your BCR pipeline on my 10x Genomics BCR sequencing data. I am able to load in the data and get as far as clustering, but when I run the pipeline (code below), I end up with an error message:

immdata <- repLoad("BCR", .mode="paired")
distBCR <- seqDist(immdata$data %>% top(500))
immdata$data <- seqCluster(immdata$data %>% top(500), distBCR, .perc_similarity = 0.9)
immdata$data %>%
  repGermline(.threads = 1)

I did some poking around with your example data set to find the differences between my data and yours. Specifically, I find that the V.name column looks different.

However, in your tutorial working with paired chain data, I see that the V.name column looks the same as mine. When I run this dataset using the functions in the BCR pipeline (seqDist, then seqCluster), I get a very similar looking error message.

file_path <- paste0(system.file(package = "immunarch"), "/extdata/sc/flu.csv.gz")
igdata <- repLoad(file_path, .mode = "paired")
distBCR_3 <- seqDist(igdata$data %>% top(500))
igdata$data <- seqCluster(igdata$data %>% top(500), distBCR_3, .perc_similarity = 0.9)
#generate germline
igdata$data %>%
  repGermline(.threads = 1)

Do you know how to fix this?

Thanks!