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

[Jesse R. <jes...@u2...>]

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