[mira_talk] Re: Questions about TCS file fields
- From: Jeremy Volkening <volkening@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 20 Mar 2011 13:48:32 -0500
For what it's worth, I've also noticed similar issues with TCS files
I've generated from mira and convert_project when trying to use them to
generate some summary statistics. See below.
On Sun, 2011-03-20 at 14:19 +0100, Bastien Chevreux wrote:
> On Saturday 19 March 2011 22:01:45 Robert Bruccoleri wrote:
> when I look
>
> > at an entry for a mapping where there are no reads, just the
> backbone,
>
> > this field has a value of 5.
>
> This seems strange. Are you sure that there are no reads?
Actually, the tcov column in my TCS files is <always> 5 for every
location, regardless of the coverage and whether it's a mapping or de
novo project.
>
> > Second, in regions where there are no reads mapped, I'm finding
>
> > coverages of more than 1, and quality scores for bases that aren't
> in
>
> > the reference. Shouldn't the lines corresponding to reference
> sequences
>
> > with no reads just have the default quality score for the backbone
> and
>
> > coverage of 1 for the base in the corresponding position in the
> backbone?
>
> Agains, this seems extremely strange. Would you have some (smaller)
> CAF of MAF which shows that?
I have also seen this same behavior. As far as I can tell, an extra base
count gets added to the "C" column for every location where there is
only backbone, no reads.
Jeremy
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