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Hi Dannon,

Thanks for telling me about that count tool.  I had not used it before.  So,
it seems the line estimates in the history windows are a bit screwy.  One
pileup file I mentioned estimated ~4,000,000 lines and the count tool showed
988,000.  And the other pileup file I mentioned estimated ~200,000 and the
count tool showed 6,382,447.  The lines totals on the cut files were off as
well, but the count tool showed consistent numbers between the pileup files
and the cut files, so I feel better.  Thanks again.

Austin

On Thu, Aug 25, 2011 at 3:19 PM, Dannon Baker <dannonba...@me.com> wrote:

> As a first step, please confirm an exact line count for the files.  See the
> "Line/Word/Character count" tool in the Text Manipulation section to do
> this.  If the estimate is significantly off, please share the history with
> me and I'll take a look to see what happened with those particular datasets.
>
> Thanks!
>
> -Dannon
>
> On Aug 25, 2011, at 6:08 PM, Austin Paul wrote:
>
> > ===> Please use "Reply All" when responding to this email! <===
> >
> > Hello,
> >
> > I am curious if the line estimation shown in the history window for
> pileup generation is at all accurate.  I am using the pileup files to
> generate expression data from bwa mapping for looking at differential
> expression, but I am having some trouble understanding the line estimates.
>  For example, for one pileup file, when I cut the reference id column and
> the number of hits column (columns 1 and 4), the number of lines in the cut
> file is about 25% that of the pileup file, and for another file it will be
> 5000%.   How can the number of lines grow 50x when I am just cutting columns
> from the file?  Shouldnt the line estimate be the same?
> >
> > Thanks,
> > Austin
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