Can Kallisto align nucleotide sequences to protein database for calculating CPM

pachterlab / kallisto

Near-optimal RNA-Seq quantification

https://pachterlab.github.io/kallisto

BSD 2-Clause "Simplified" License

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Can Kallisto align nucleotide sequences to protein database for calculating CPM #453

Open xiaohong88999 opened 3 months ago

xiaohong88999 commented 3 months ago

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: 1722518660694

Yenaled commented 3 months ago

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

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