I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the same sample (merging reads with PEAR, removing low quality with Trimmomatic and removing RNA with SortMeRNA). What I would like to do now is to check the expression of the genes in my MAGs with the metatranscriptomics of the sample (hope it's clear enough). I aligned metatranscriptomics reads to each MAG and retained only those reads that aligned (used BOWTIE2). Now I am thinking of doing a functional analysis to check what genes are expressed in each MAG. However, I have no idea how and where to start. Was the alignment even a good idea? How would you tackle this problem?
My idea is to try TransDecoder on these aligned transcriptomics reads to get the ORFs and cluster them with CD-HIT2. Then perform a functional analysis as normal with KEGG/InterProSCAN/Blast etc. Would this be a correct way to go?
Your advice will be highly appreciated.