Question: Mapping Reads Back To Assembly Contigs To Generate Pileup
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gravatar for Sen
7.4 years ago by
Sen0
Sen0 wrote:

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!

pileup bwa coverage • 2.2k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 7.4 years ago by Sen0

How are you calculating the coverage?

ADD REPLYlink written 7.4 years ago by Vikas Bansal2.3k
0
gravatar for Swbarnes2
7.4 years ago by
Swbarnes21.5k
Swbarnes21.5k wrote:

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

ADD COMMENTlink written 7.4 years ago by Swbarnes21.5k
0
gravatar for Stevelor
7.4 years ago by
Stevelor310
Stevelor310 wrote:

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

HTH?

Cheers! Steve

ADD COMMENTlink written 7.4 years ago by Stevelor310
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