junction_saturation.py resampling

[mehr...@broadinstitute.org]

Hello,

To check junction saturation, junction_saturation.py works as follows (from the manual):

This module checks for saturation by resampling 5%, 10%, 15%, ..., 95% of total alignments from BAM or SAM file, and then detects splice junctions from each subset and compares them to reference gene model.

In resampling, are the reads/read alignments shared? 

I mean, in resampling for 5%, and incremental resampling for example 15%, the read alignments used for 5%, can still be (re)used in 15% and so on? So their is no guarantee that each time resampling is performed, 'new' read alignments will be used? 

Thanks,

SM

[Liguo Wang]

Yes they are shared, Since we are resampling all the way to 95%. 

Liguo

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[mehr...@broadinstitute.org]

Thank you for confirming this!