How to use metagenomic MAGs to align metatranscriptomic reads to obtain TPMs.

[zx1474]

Hi,
How to align metagenomic reads obtained from MetaBAT-generated MAGs to metatranscriptomic reads in order to calculate the Transcripts Per Million (TPM) for these MAGs.
$ salmon index -i transcripts_index -k 31 --gencode -p 8 -t /home/MBR02_0-5cm.6.fa
$ salmon quant -i transcripts_index -l A -1 /home/transcriptom/PCBR/PCBR_p_r1.fastq -2 /home/transcriptom/PCBR/PCBR_p_r2.fastq --validateMappings -o transcripts_quant

This is my code, but it’s doing the opposite of what I expected because it calculates the TPM as if the genome were a single entity.I’m not sure if the genome.fa file should be used as the index.