Mapping Reads Back To Assembly Contigs To Generate Pileup
I am trying to map the raw reads of a genome back to its assembled genome to generate the pileup. I downloaded the raw reads (fasta and qual files) from NCBI Trace Archive. Because they are long reads, I used BWA to align them against the assembled genome. I used samtools to generate the pileup. Everything was done with default values. The problem I am having is that the assembly I got has a 20X coverage, while the reported coverage in the original paper was ~12x. I am really puzzled by this big difference. Anyone can help? Thanks very much!
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How are you calculating the coverage?