Re: [Useq-users] base-by-base read coverage stats

[David N. <dav...@gm...>]

Your read sizes shouldn't change thus its easy to get start and stop for
each read when you know the center position.

The ReadCoverage app does just this and calculates a per base read coverage.
It throws a warning if it finds reads of different lengths.

-cheers, D


On 3/15/11 1:14 PM, "Andrew Oler" <And...@hc...> wrote:

> Hi David,
> 
> I have another question.  For the NovoalignParser (and other parsers, such as
> Tag2Point), the documentation says that it converts to "center position binary
> point data", but to get a base-by-base read coverage, we would need start and
> stop positions for each read, especially when reads have different sizes.  Has
> the format of the bar file been updated to include start and stop or is it
> still center-based?  If not, do you have a recommended method for getting
> base-by-base read coverage?
> 
> Thanks,
> 
> Andrew
> 
> Brad Cairns Lab
> Huntsman Cancer Institute Room #4350
> University of Utah
> 2000 Circle of Hope
> Salt Lake City, UT 84112
> (801) 585-1823
> 
> From: David Nix <Dav...@hc...<mailto:Dav...@hc...>>
> Date: Tue, 15 Mar 2011 10:36:01 -0600
> To: Andrew Oler <and...@hc...<mailto:and...@hc...>>
> Subject: Re: Novo bis parser
> 
> It means exactly what it says.  Where there is an overlap in a pair of reads
> from the same template it calls a consensus so that you don¹t double count the
> same base pairs.
> 
> Yes, 0.41 is a lot of overlap, the library insert size was too small and thus
> your effectively cutting your data output by 40%.  This should be < 5%.
> 
> -cheers, D
> 
> 
> On 3/14/11 10:15 AM, "Andrew Oler" <And...@hc...> wrote:
> 
> Hi David,
> 
> I'm running NBP and I was wondering if you could explain the stats at the end.
> 
>> From the app description, what does this mean, exactly?  "Flattens
>> overlapping reads in a pair to call consensus bps."  Does that mean to call
>> consensus as to whether converted or not?  If overlapping, then it should
>> have a higher accuracy right?
> 
> I got these stats at the end.
> 
> 2353965845 BPs overlapping paired sequence
> 5645468238 BPs paired sequence
> 0.417 Fraction overlapping bps from paired reads.
> 
> This means that I had a lot of overlapping reads, right?   What do you usually
> get for this number?
> 
> Is there a way to get coverage statistics, e.g., what fraction of the genome
> is covered at least 5-fold?  Or coverage tracks?
> 
> Thanks,
> 
> Andrew
> 
> Brad Cairns Lab
> Huntsman Cancer Institute Room #4350
> University of Utah
> 2000 Circle of Hope
> Salt Lake City, UT 84112
> (801) 585-1823
> 
> 
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