Hi,
I have aligned 10 metagenomic samples(WGS --> 2x150bp) to a bacterial reference genome to get the coverage for that specific bacterial reference.
My 10 samples have different number of reads as expected.
I have used bwa to align those 10 samples to my reference genome. The thing is that coverages are different but how do you account for library size variation when computing the coverage
For example reads for Sample 1 aligned to my reference genome had a mean coverage of 25. On the contrary Sample 2 had a mean coverage of 15.
Since samples 1 and 2 had different number of reads how do i know the difference between a coverage of 25 and 15 is real or is due to library size ???
The question i´m trying to answer is the number of bacterial genomes you have in SAMPLE1 is really different from the number found in SAMPLE10. For me, the mean coverage corresponds to the number of bacterial genomes you have in your Sample. Thanks
