Tutorial:Importing multiple .h5 files using tximport
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@nelsonsgarcia-15764
Last seen 16 months 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.

tximport Tutorial • 955 views
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Thanks. How can I create the vector?

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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")
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@mikelove
Last seen 11 hours ago
United States

That’s just demo code which points to the demo files. All you need to do is have files point to your h5 files, however you want to create that vector.

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