identification of catabolic genes in soil metagenome shotgun data
I have 4 shotgun sequencing data of soil microbial communities. I have compiled a custom database of genes of polyciclic aromatics catabolism and mapped my raw shotgun reads to this database. So from each sample I obtained reads corresponding to PAH catabolic genes. For example:
sample 1 - 100 reads
sample 2 - 200 reads
sample 3 - 300 reads
sample 4 - 150 reads
And the question is: can I, based on the number of reads, make conclusions about the number of genes in the samples? I.e. can I say, that the sample 3 contains more PAH genes than sample 1? Also I have carried out the taxonomic analysis, but as for the genes, it's not so obvious.
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