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

[Walenz, B. <bw...@jc...>]

Hi-

I had to run one myself, and then check the code.

There is a definite uninitialized value problem here.  In effect, any gap in
the scaffold was not set to zero coverage.  I've fixed it in CVS.  If you're
not using CVS, patch AS_RUN/fragmentDepth.c by adding

memset(histogram, 0, sizeof(uint32) * histogramMax);

near the start of the computeStuff() function (line 71 - after the block of
variables are defined, before the first 'if' test works).  The patch in CVS
is slightly different, but equivalent.

Big scaffolds (with few gaps) didn't seem to be affected too much.  Small
scaffolds - yours are two contigs joined by a fosmid? - were.

I'm stunned this has survived for so long!  Thanks for noticing.

b


On 8/9/12 10:23 AM, "Christoph Hahn" <chr...@gm...> wrote:

> 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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