Mapping Reads Back To Assembly Contigs To Generate Pileup

Question

[Sen]

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!

[Vikas Bansal]

How are you calculating the coverage?

Answer 1

[Swbarnes2]

They might have trimmed out more low-quality reads or repetative reads than you did.

Answer 2

[Stevelor]

we did the same a few weeks ago....[?]try RazerS You can define different sensitivities...works fine on our data

HTH?

Cheers! Steve