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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:

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> 
> 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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