Hi,
Beginner here. I have Illumina RNA seq reads from an insect and I would like to analyze the microbiome composition within the insect transcriptome. All the papers I have read that look into the microbiome of an organism only use QIIME with the metagenome. I can't find any examples where the transcriptome is used as input for QIIME. Any help and suggestions for tools or workflows would be greatly appreciated.