problem in cyverse kallisto & sleuth apps

Question

[규희]

Hi, I'm using Kallisto-v.0.43.1 and RStudio_Sleuth_pb tools for Rna-seq analysis in Cyverse. I'm asking you because there are some problems.

1. I want to download the kallisto output file, abundance.h5 to my window and analyze it in my rstudio, but I have error "Error in H5Fopen(file): HDF5. File accessibility. Disable to open file."
2. In RStudio_Sleuth_pb, I don't use sleuth_pb_tutorial.Rmd, I just enter the code into rscript to analyze kallisto outputs. The PCA plot is drawn well, but when I use the function "plot_sample_heatmap()", it does not appear in rstudio plot.
3. When drawing a heatmap in the shiny browser using sleuth_live(), it is not drawn when the target id is more than about 200.
4. I want to adjust the heatmap size or scale options when drawing heatmap in shiny browser using sleuth_live(), but I don't know how. If there is a solution to the above 4 problems, please reply. Thank you.

[dsull]

The only suggestions I can offer is to update kallisto and sleuth to their latest versions (0.48.0 and 0.30.0, respectively) and also update rhdf5 to the latest version. And then regenerate the hdf5 file.

More suggestions here: https://github.com/pachterlab/sleuth/issues/120