I have some Kallisto output, and I want to apply tximport on the abundance.tsv file. However, I don't understand why my output is like this, not having target IDs, while using correctly how the manual prescribed:

kallisto quant -b 10 -i Homo_sapiens_index -o ERX3307771_quant -t 1 --single -l 51 -s 1 -g Homo_sapiens.GRCh38.101.gtf ERX3307771.fastq

I think we need those target IDs to be not 0 1 2 3... in order to be able to apply tximport.

Does someone know what could be wrong here?

(I'm very new to bioinformatics)

Kindest regards Julie

Cross-posted and answered on Biostars: https://www.biostars.org/p/473083/