Hello everyone. In a DEG project involving salmon,tximport, and DESeq2 tools, I achieved a 62% mapping rate when using salmon in mapping-mode. However, this rate increased to 97% when using the alignment-mode of salmon. So I decided to see if there are any DEGs between the two modes. However, I encountered an error indicating index differences in the tximport package while trying to import the count data into DESeq2. Do you have any suggestions on how to overcome this error?

reading in files with read_tsv
1 2 3 4 5 Error in tximport(files = mapped_vs_aligned, type = "salmon", tx2gene = ensg_ve_enst,  : 
  all(txId == raw[[txIdCol]]) is not TRUE
In addition: Warning message:
In txId == raw[[txIdCol]] :
  longer object length is not a multiple of shorter object length

You apparently have files with different numbers of transcripts. The error comes from the part of tximport that compares the transcripts in the first file to the transcripts in the remaining files.