How to use Sleuth for Kallisto results in one directory?

Question

[weixiaokuan]

Hi, I am trying to use sleuth to analyze a set of results generated by kallisto. However, all the results (abundance tsv files) are in one directory. I know that for regular analysis, we create a sample file which indicates one directory for each kallisto output.

But now I have all the kallisto results in one directory. Could someone give me some advice how to handle this situation? I don't want to make hundreds of directories and put every kallisto file to each directory. Thank you. -Xiaokuan

Answer 1

[dsull]

In the data frame you supply to sleuth_prep, your 'path' column contains the names of your tsv files.

So you can name your kallisto tsv files sample1.tsv, sample2.tsv, sample3.tsv, etc. in a single directory and simply put those file names into the path column of the data frame.

[weixiaokuan]

@dsull, thank you for your response. It seems get the command going but I got another error related to HD5 file.

"Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file."

Is that because for my data sets from Kallisto, I only have abundance tsv files but no hd5 files? How may I bypass this? Thank you.