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Tutorial: Importing multiple .h5 files using tximport
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gravatar for nelson.s.garcia
15 days ago by
nelson.s.garcia0 wrote:

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.

ADD COMMENTlink modified 14 days ago by Steve Lianoglou12k • written 15 days ago by nelson.s.garcia0

Thanks. How can I create the vector?

ADD REPLYlink written 14 days ago by nelson.s.garcia0

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")
ADD REPLYlink written 14 days ago by Michael Love17k
0
gravatar for Michael Love
15 days ago by
Michael Love17k
United States
Michael Love17k wrote:

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.

ADD COMMENTlink written 15 days ago by Michael Love17k
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