Question: Error with tximport on Kallisto .h5 data.
gravatar for srdjan.kasapovic0
17 months ago by
srdjan.kasapovic00 wrote:

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!

ADD COMMENTlink written 17 months ago by srdjan.kasapovic00

Can you post sessionInfo and all of your code?

ADD REPLYlink written 17 months ago by Michael Love23k
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