HI, I have a gut metagenomics sample (WGS from illumina 2x150bp). The following custom pipeline has been applied:
1 - Filtered my reads (to remove human contaminants and phiX) 2- Assembly with Megahit to get contigs 3 - Binning megahit contigs with metabat 4- Gene prediction on contigs with prodigal (got genes and proteins) 5- Assigned taxonomy to the (bins or genes) with Kaiju
The thing is how can i get the relative abundance for the species present in the sample. Should i map each of my genes back to my reads and simply count the mapped reads. Then divide the number of mapped reads by the total number of reads to get the relative abundance. For example if i get 100000 reads mapped to one gene and my sample has 1M reads than i can assume that the relative abundance of that species is 10% ?? Am i correct or how would you get the relative abundance ?
Thanks for your comments.