Hello, I have run a metagenomics DNAseq WGS (2*150bp ) experiment with 20 feacal samples (10 disease and 10 control) from different patients. I have aligned the reads back to a reference bacterial genome.
I would like to compare the control group to the disease group and see if i can find differences on the bacterial genes. First approximation would be present/absent and later SNPs....
What i have done:
- ALign patients and controls reads to the reference bacterial genome
- Used featuresCount (-p with fragments) to get counts. Not using multimap (Is that correct ?)
- Used the output matrix from featuresCount as input to DESEq.
- Normalized data with Deseq and compared group with deseq using control vs disease as contrasts.
Is that correct ?? Note that this not RNA data but DNA data. Is the normalization approriate in such context
Thanks for advise.