I mapped a depleted metatranscriptome bam file against a reference bacterial genome. Some genes have a 'substantial' number of reads mapping. I have previously isolated this bacteria from the sequencing site. Is there a method where I could say that x number of genes from this bacteria are expressed, therefore this bacteria is functionally active within the microbiome?
I have looked at the mapping data in Artemis and some genes are expressed >1000 times. How may reads constitute evidence of expression in a metatranscriptome?