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nelson.s.garcia
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@nelsonsgarcia-15764
Last seen 5.0 years ago
I am having trouble with importing kallisto files for DESeq analysis in R. I went to the tutorial website and found this:
files <- file.path(dir, "kallisto_boot", samples$run, "abundance.h5")
names(files) <- paste0("sample", 1:6)
txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE)
head(txi.kallisto$counts)
I have fifteen .h5 files to import in total. I can't quite figure out how to do it with the R script above.
Is "kallisto_boot" something that I need to make prior to importing the files?
What does samples$run do?
Should I replace "abundance.h5" with the fifteen .h5 files that I need to import?
Thank you very much.
Thanks. How can I create the vector?
It's a character vector that lists the files.
First you need to locate the files on your laptop or cluster and make sure that you point to them correctly (either using relative or absolute paths).
files <- c("/path/to/file1.h5", "/path/to/file2.h5")