Error with tximport on Kallisto .h5 data.
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@srdjankasapovic0-14589
Last seen 4.8 years ago

Hello all,

I am working on differential expression benchmarking and I use tximport to read in the data from Salmon/Sailfish/Kallisto/RSEM.

Sample data is always the same, only different quantification or alignments tools are used. Everything besides abundances.h5 import works fine. I do have rhdf5 library installed and running. I can read in the data from Kallisto's TSV files, but when I try to do the same with .h5 I get:

 

Error: all(c(lengthCol, abundanceCol) %in% names(raw)) is not TRUE

 

Is there any reason why it wouldnt work with h5 files? Any way around this? Thanks!

tximport kallisto bioconductor rnaseq • 712 views
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Can you post sessionInfo and all of your code?

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