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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