Hi All, I used Kallisto to generate transcript abundance files for RNASeq data and am trying to run it through DESeq2. My input is 4 .tsv files as well as a .gene_trans_map file, and the following error message is generated:
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
*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!