I am processing Alevin-Seurat for scRNA-seq analysis using following code:

    colon_file <- "//wsl.localhost/Ubuntu/home/cancer/quant/SRR1/alevin/"
    list.files(colon_file)
    colon_dge <- tximport(colon_file, type="alevin")

output:

    > list.files(colon_file)

[1] "alevin.log"          "featureDump.txt"     "quants_mat.gz"       "quants_mat_cols.txt" "quants_mat_rows.txt"
[6] "quants_tier_mat.gz"  "whitelist.txt"

An error occurs:

Error: lexical error: invalid char in json text.
                                       \\wsl.localhost/Ubuntu/home/cancer
                     (right here) ------^

I am running this code in an R environment, not in WSL. How can I solve this issue?

Two things:

1) See https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Alevin -- Your colon_file must point to the quants_mat.gz file and not to only the enclosing folder.

2) Are you running R in Windows? Usually you can access files via "//wsl$/<distro_name>/home/<username>/your_file..."