Can Kallisto align nucleotide sequences to protein database for calculating CPM

[xiaohong88999]

We have download many metagenome fastq files and need to align them to a custom protein database for calculating CPMs. We use 'kaliisto index --aa' command to build index from our FASTA-file containing amino acid sequences. Then we use 'kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq pairB_1.fastq pairB_2.fastq ' command to get count an CPM. But it failed many times. Details as below:

[Yenaled]

You should be using kallisto bus --aa for pseudoalignment.

Recommend that you use the kb-python program for these purposes.