When I run BWA using the transcriptome (sortmerna.fq file) against the assembled transcriptome (megahit.contigs.fa), then the resulting annotation (sam file) has a bunch of k-mer names like k141_38650 instead of gene IDs. But if I run BWA with a difference reference file so that the sam file has gene IDs, then the input won't go into salmon. Is there a way to identify and label the k-mers with gene IDs? If not, how can I get the identity of the differentially expressed k-mers?

BWA that gives gene IDs but cannot go into salmon:

bwa index -a bwtsw  microbial_all_cds.fasta
bwa mem -t 32 microbial_all_cds.fasta Sample.contigs.fa > Sample_annotation_bwa.sam 

BWA that successfully goes into salmon but gives k-mers:

bwa index -a bwtsw Sample1_megahit.contigs.fa
bwa mem -t 32 Sample1_megahit.contigs.fa Sample1-sortmerna.fq > Sample1_megahit.annotation_bwa.sam

Salmon:

./salmon-1.8.0_linux_x86_64/bin/salmon quant -p 12 -t Sample1_megahit.contigs.fa -l A -a Sample1_megahit.annotation_bwa.sam -o Sample1_salmon

Thank you!