===> Please use "Reply All" when responding to this email! <===
Sure, no problem. Those estimates are indeed way off, ideally they're
within about 10% of the actual count. Would you mind sharing the
history with me at this email address so that I might take a look and
figure out where the estimation went wrong? Thanks!
-Dannon
On 08/25/2011 06:33 PM, Austin Paul wrote:
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
<mailto: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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___________________________________________________________
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