Kallisto bus out put doesn't change for --cm flag

[tsofiya]

A while ago I asked about getting the raw, not collapsed gene matrix (#408), and was answered I should use -cm flag.
On my current project I wanted to do the same so I run kallisto bus twice, once with -cm and once without.
my script:

kallisto bus -i cdna.idx -o results/bustools/ -x 0,0,8:0,8,21:1,0,0 -t 8 GE_S1_L001_R1_001.fq.gz GE_S1_L001_R2_001.fq.gz GE_S1_L002_R1_001.fq.gz GE_S1_L002_R2_001.fq.gz

cd results/bustools

mkdir -p tmp
bustools sort -o tmp/output.s.bus -T tmp -t 8 -m 4G output.bus

bustools inspect -o inspect.json -w path/to/whitelist.txt tmp/output.s.bus

bustools correct -o tmp/output.s.c.bus -w path/to/whitelist.txt tmp/output.s.bus

bustools sort -o output.unfiltered.bus -T tmp -t 8 -m 4G tmp/output.s.c.bus

mkdir -p counts_unfiltered

bustools count -o counts_unfiltered/cells_x_genes -e matrix.ec -t transcripts.txt --genecounts output.unfiltered.bus -g path/to/kalisto_t2g.txt

rm -rf tmp

(when I run with -cm I use a different folder name)

Later, I use an R script to read the matrix:

read_count_output <- function(dir, name) {
  dir <- normalizePath(dir, mustWork = TRUE)
  m <- readMM(paste0(dir, "/", name, ".mtx"))
  m <- Matrix::t(m)
  m <- as(m, "dgCMatrix")
  ge <- ".genes.txt"
  genes <- readLines(file(paste0(dir, "/", name, ge)))
  barcodes <- readLines(file(paste0(dir, "/", name, ".barcodes.txt")))
  colnames(m) <- barcodes
  rownames(m) <- genes
  return(m)
}


mat <- read_count_output(paste0(project.dir, results.dir,"/bustools/counts_unfiltered"), name="cells_x_genes")
rownames(mat)<- sub("\\..*", "", rownames(mat))

tr2g <- read_tsv("t2g.txt", col_names = c("transcript", "gene", "gene_symbol")) %>%
  select(-transcript) %>%
  distinct()
tr2g$gene<- sub("\\..*", "", tr2g$gene)


rownames(mat) <- tr2g$gene_symbol[match(rownames(mat), tr2g$gene)]
my.data.no.dup= rowsum(mat, row.names(mat))

and the same with the -cm matrix.

The problem is- I'm getting the exact same matrix!
This didn't happened before. Am I doing something wrong?

[Yenaled]

Are you using cm with bustools count or kallisto bus?