You don't really need a file called samples.txt. You just need a
data.frame that contains columns that describe pertinent information about your samples, where the
row.names of the
data.frame are the same as your samples. You could recreate the
data.frame used in the DESeq2 vignette like this:
> samps <- paste0("ERR", 188000 + c(297, 88,329, 288, 21, 356)) > samps  "ERR188297" "ERR188088" "ERR188329" "ERR188288" "ERR188021" "ERR188356" > z <- data.frame(pop = rep("TSI", 6), center = rep("UNIGE", 6), run = samps, condition = rep(c("A","B"), each = 3), row.names = samps) > z pop center run condition ERR188297 TSI UNIGE ERR188297 A ERR188088 TSI UNIGE ERR188088 A ERR188329 TSI UNIGE ERR188329 A ERR188288 TSI UNIGE ERR188288 B ERR188021 TSI UNIGE ERR188021 B ERR188356 TSI UNIGE ERR188356 B
And you could then proceed as per the vignette. You would obviously need to do something tailored to your experiment, but that's the idea.