Re: [wgs-assembler-users] coverage information for scaffolds/contigs

[Christoph H. <chr...@gm...>]

Hi Brian,

thanks for your reply! The fragmentDepth utility does basically what I 
was interested in, thanks! I am a little confused with its output, 
though. If I run it in -scaffold mode like:
fragmentDepth -scaffold < *.posmap.frgscf.sorted

In the fragmentDepth output I get the following as an example:
uid     start   end     mode    mean    median
7180006953248   0       33010   40294   42.589286       2
7180006953249   0       31936   1518    42.845247       1
7180006953250   0       26539   62454   41.643727       41

A few questions there:
What exactly is the mode (40294,1518,62454) column? According to 
*.posmap.scflen scaffold 7180006953248 is 33204 long - why does it 
calculate the coverage only until position 33010? Also, I am not sure 
how to understand the median value. To reach a value of 1 or 2 as in the 
first two scaffolds in the example about half of the positions need to 
have a coverage of 0-1 or 0-2, right? can that be correct, or am I 
misunderstanding something here?

Thanks for your help!

cheers,
Christoph



On 08/09/2012 05:03 AM, Walenz, Brian wrote:
> Hi, Christoph-
>
> [Sorry, wrote this 16 hours ago and forgot to send]
>
> Check out the 'fragmentDepth' utility.  It computes coverage, and outputs in
> three different ways: coverage of each scaffold, a histogram of coverage (as
> at the end of *.qc), and a fasta-like output of the actual depth of coverage
> at each base in the scaffold.
>
> I can't think of a reason it would fail on contigs, but I haven't tried it.
>
> The posmap files should be capturing most of the important stuff from the
> (agreed: very difficult to use) asm file.  If you can't get what you're
> looking for out of the posmap files, we need to add to them.
>
> b
>
>
>
> On 8/8/12 6:20 AM, "Christoph Hahn" <chr...@gm...> wrote:
>
>> Hello CA developers and experts,
>>
>> I have just finished my first big 454+illumina hybrid assembly using CA7
>> and I am about to assess the result now in comparison to purely illumina
>> based assemblies.
>>
>> One question there: What is the easiest way to get coverage information
>> for the scaffolds, contigs, unitigs in the *.scf.fasta, *.ctg.fasta,
>> etc. files? I figured, that it is possible to calculate it manually
>> using the information in the *.posmap.frgscf and *.posmap.scflen files
>> (in case of scaffolds). I guess, the information is also in the *.asm
>> file, but I am having problems reading/parsing the file.
>> Is there an easy way you can think about?
>> The reason, why I want to do this is that I want to bin the
>> scaffolds/contigs based on coverage, GC-content and length.
>>
>> Any ideas are highly appreciated, thanks!
>>
>> Much obliged,
>> Christoph
>>
>> University of Oslo, Norway
>>
>>
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