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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