tximeta parse error

Question

[n.tear]

Running the following code:

dir <- "C:/Users/Natha/Documents/PhD/SalmonQuantsBatch123"
list.files(dir)
list.files(file.path(dir, "quants"))

#if file is located in another location you can do 
#dir <- "Z:/appropriatefolder"
#csvfile <- file.path(dir, "sample_table.csv")
coldata <- read.csv("SampleInformation.salmon.csv", row.names=1, stringsAsFactors=FALSE)
coldata

coldata$names <- coldata$run
coldata$files <- file.path(dir, "quants", coldata$run, "quant.sf")
file.exists(coldata$files)

library("tximeta")
se <- tximeta(coldata)

Creates the following error...

Error in parse_con(txt, bigint_as_char) : parse error: premature EOF

                     (right here) ------^

How can I solve this issue?

Answer 1

[Kevin Blighe]

I am guessing that this is a line-end ('end-line') / carriage return issue. Your files were probably created on Mac or Linux, but you are now processing them on Windows. You could ask your collaborator (whoever that may be) to first run unix2dos on all files before sending them to you.

Kevin