I run PeakShiftFinder (v3.9) on my data using default parameters. I get this message:
Fetching stranded PointData...
Picking peaks...
chrUn
Exception in thread "main" java.lang.NullPointerException
at edu.utah.seq.data.PointData.subSamplePointData(PointData.java:589)
at edu.utah.seq.analysis.PeakShiftFinder.pickPeaks(PeakShiftFinder.java:215)
at edu.utah.seq.analysis.PeakShiftFinder.findPeakShift(PeakShiftFinder.java:82)
at edu.utah.seq.analysis.PeakShiftFinder.<init>(PeakShiftFinder.java:62)
at edu.utah.seq.analysis.PeakShiftFinder.main(PeakShiftFinder.java:513)
Do you know what happened? Is it something to do with reads aligning with unmapped sequence in mouse genome?
Unrelated question - the users interface beta in v3.9 was abandoned in v4.0 archive. Any reason?
Thank you for help!
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Hmm. First, an easy answer, nope, the GUI hasn't been abandoned. It just didn't make it into 4.0. It's still in beta testing. Once its thoroughly debugged, we'll make it a standard addition. For the time being just place the GUI_DoubleClickMe_Beta.jar file in your USeq_4.0 folder and it will work. You will need to reset the path to the USeq_4.0 folder in the preferences though. The bugs present relate to the user interface and not the analysis applications that the application wraps. The UI needs some work on user friendliness!
As far as problems with PeakShiftFinder.... Try removing chrUn from your point data. I suspect that has only a few data points on one strand and the application is trying to find the other strand. If that doesn't work then I'd appreciate it if you would deidentify your data and send it to me and I'll debug it from here (david.nix@hci.utah.edu).
-cheers, David
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I run PeakShiftFinder (v3.9) on my data using default parameters. I get this message:
Fetching stranded PointData...
Picking peaks...
chrUn
Exception in thread "main" java.lang.NullPointerException
at edu.utah.seq.data.PointData.subSamplePointData(PointData.java:589)
at edu.utah.seq.analysis.PeakShiftFinder.pickPeaks(PeakShiftFinder.java:215)
at edu.utah.seq.analysis.PeakShiftFinder.findPeakShift(PeakShiftFinder.java:82)
at edu.utah.seq.analysis.PeakShiftFinder.<init>(PeakShiftFinder.java:62)
at edu.utah.seq.analysis.PeakShiftFinder.main(PeakShiftFinder.java:513)
Do you know what happened? Is it something to do with reads aligning with unmapped sequence in mouse genome?
Unrelated question - the users interface beta in v3.9 was abandoned in v4.0 archive. Any reason?
Thank you for help!
Removing chrUn did help.
Thank you
Hmm. First, an easy answer, nope, the GUI hasn't been abandoned. It just didn't make it into 4.0. It's still in beta testing. Once its thoroughly debugged, we'll make it a standard addition. For the time being just place the GUI_DoubleClickMe_Beta.jar file in your USeq_4.0 folder and it will work. You will need to reset the path to the USeq_4.0 folder in the preferences though. The bugs present relate to the user interface and not the analysis applications that the application wraps. The UI needs some work on user friendliness!
As far as problems with PeakShiftFinder.... Try removing chrUn from your point data. I suspect that has only a few data points on one strand and the application is trying to find the other strand. If that doesn't work then I'd appreciate it if you would deidentify your data and send it to me and I'll debug it from here (david.nix@hci.utah.edu).
-cheers, David