thx dsull for the explanation. that makes sense. I manage to create the drosophila genome using the following command (I copied it from your github repository.
but if you look at the examples given by the people created the example indicies, they also took the dna and not the cdna to create the index in version 0.50.
I was the one who created those indices and I replied to you on the GitHub issues. My reply is reproduced below:
This indices were created by kb-python: kb-python takes in the GENOME fasta and extracts a TRANSCRIPTOME fasta from it (and then calls the kallisto index command on the TRANSCRIPTOME fasta that it just extracted).
If you don't use kb-python and simply stick with calling the kallisto index command, then you should be using the TRANSCRIPTOME fasta. The kallisto index command always uses the TRANSCRIPTOME fasta.
but if you look at the examples given by the people created the example indicies, they also took the dna and not the cdna to create the index in version 0.50.
see kallisto-transcriptome-indices
The files they are using are all dna primary assembly files, no cdna.
I was the one who created those indices and I replied to you on the GitHub issues. My reply is reproduced below:
This indices were created by
kb-python: kb-python takes in the GENOME fasta and extracts a TRANSCRIPTOME fasta from it (and then calls thekallisto indexcommand on the TRANSCRIPTOME fasta that it just extracted).If you don't use kb-python and simply stick with calling the
kallisto indexcommand, then you should be using the TRANSCRIPTOME fasta. Thekallisto indexcommand always uses the TRANSCRIPTOME fasta.