Hello,

I am importing kallisto output files into R through tximport package and then using DESeqDataSetFromTximport() funstion. I am following the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).

So, first to construct the tx2gene table for linking transcripts to genes, I did as below (based on Tximport vignette):

library(tximportData)
dir <- system.file("extdata", package = "tximportData")
list.files(dir)
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))

Parsed with column specification:
cols(
  TXNAME = col_character(),
  GENEID = col_character()
)
#
  

Then, I did as below to read my meta data file:

datadir <- "/scratch/fs/ye/"
meta <- read.delim(paste0(datadir, "/ye_meta.txt"),
                   header = TRUE, as.is = TRUE)
rownames(meta) <- meta$names
meta$trt <- factor(meta$trt)
meta$cell <- factor(meta$cell)

Finally, to do tximport, I ran as follows, however, I got the below Error:

kallistofiles <- file.path(datadir,"/kallisto/", meta$names, ".*-abundance.tsv")
names(kallistofiles) <- meta$names
txi <- tximport(kallistofiles, type="kallisto", tx2gene=tx2gene)

Error in tximport(kallistofiles, type = "kallisto", tx2gene = tx2gene) : all(file.exists(files)) is not TRUE

So, I performed file.exists() as suggested in another post:

file.exists("tx2gene")

[1] FALSE
  

file.exists(kallistofiles)

[1] FALSE FALSE FALSE FALSE FALSE FALSE
  

However, when I only run kallistofiles, it can read my kallistofiles:

kallistofiles

                                                    SRR6822797
"/scratch/fs/ye///kallisto//SRR6822797/.*-abundance.tsv"
                                                    SRR6822798
"/scratch/fs/ye///kallisto//SRR6822798/.*-abundance.tsv"
                                                    SRR6822799
"/scratch/fs/ye///kallisto//SRR6822799/.*-abundance.tsv"
                                                    SRR6822800
"/scratch/fs/ye///kallisto//SRR6822800/.*-abundance.tsv"
                                                    SRR6822801
"/scratch/fs/ye///kallisto//SRR6822801/.*-abundance.tsv"
                                                    SRR6822802
"/scratch/fs/ye///kallisto//SRR6822802/.*-abundance.tsv"
  

I would highly appreciate if you can help me how to solve this Error. Thanks you so much.