Re: [Useq-users] subsample or normalize worked into sam2useq?

[David N. <dav...@gm...>]

Hmmm, Sam2USeq by default scales the data based on the total number of
reads.  Thus making relative read depth/coverage graphs.  You can then
reformat these to big wig using the USeq2UCSCBig app.

Are you looking for something different?

-cheers, D

On 5/2/12 4:51 PM, "Jesse Rowley" <jes...@u2...> wrote:

>We have noticed that visualization of comparisons in IGB can lead to
>confusion when comparing samples that aren't normalized to total aligned
>reads prior to making depth coverage tracks.  The steps that we use to
>get normalized Read Coverage tracks to visualize in IGB  are SamParser,
>SubSamplePointData, ReadCoverage.  This is a carryover from when we were
>using .novoalign format files and seems rather inefficient.  Could this
>option (either subsample to a user defined number, or just scale the
>depth coverage tracks to a user defined %)  be worked into the Sam2Useq?
>thanks,
>
>Jesse Rowley
>Post-Doctoral Research Fellow
>Andrew Weyrich Lab
>Eccles Institute of Human Genetics
>University of Utah
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