Hi All, I used Kallisto to generate transcript abundance files for RNASeq data and am trying to run it through DESeq2 (all on Galaxy). My input is 4 .tsv files as well as a .gene_trans_map file, and the following error message is generated:
Note: importing abundance.h5 is typically faster than abundance.tsv
reading in files with read.delim (install 'readr' package for speed up)
1 2 3 4
removing duplicated transcript rows from tx2gene
Error in $<-.data.frame(*tmp*, "TXNAME", value = character(0)) :
replacement has 0 rows, data has 510059
Calls: get_deseq_dataset -> $<- -> $<-.data.frame
I have tried changing a variety of parameters, including setting header to false, and I have also tried only using one dataset per factor level, and nothing is working to fix this error. I have also tried using a .gff3 file rather than a .gene_trans_map file, and that also is not making a difference. Any advice would be much appreciated.
