Hi, I met some trouble when using kallisto to analyse homologous genes expression. In my case, sample1 and sample2 are two varieties with very similar genome sequence. I merged the transcript fasta files of these two samples, then I ran kallisto using paired-end reads of sample1. Kallisto worked successfully. In the aboudence.tsv file, I compared the TPM value of homologous genes in sample1 and sample2, though many genes in sample2 were much lesser than sample1, there were a part of genes showed higher TPM value in sample2 than sample1. This confused me whether I made some mistake in analysis procedures or kallisto could not effectively figure out this project?
Thank you very much!