Etchevers:Notebook/STRA6 in eye development/2009/06/30: Difference between revisions
No edit summary |
mNo edit summary |
||
Line 130: | Line 130: | ||
*'''[[User:Etchevers|Heather]] 02:48, 30 June 2009 (EDT)''': | *'''[[User:Etchevers|Heather]] 02:48, 30 June 2009 (EDT)''': | ||
On the [http://vancouvershortr.wiki.sourceforge.net/WorkFlows Workflows] page for FindPeaks, as a neophyte I would have found it really useful if Anthony added in the expected output. I will give it a try and see. | ''On the [http://vancouvershortr.wiki.sourceforge.net/WorkFlows Workflows] page for FindPeaks, as a neophyte I would have found it really useful if Anthony added in the expected output. I will give it a try and see. | ||
I keep aborting this entry by accident - it's really frustrating. Anyhow, will try -qualityfilter 10 since recommended 10-20 and 30 was used in example. All parameter/flags are [http://vancouvershortr.wiki.sourceforge.net/FP4Parameters here] and -saturation is particularly interesting. | |||
I also don't know whether the Monte Carlo or the Lander-Waterman false detection rate calculations are more adapted, when I don't have a control file (want to use ISL1 but that is an ELAND format). | I also don't know whether the Monte Carlo or the Lander-Waterman false detection rate calculations are more adapted, when I don't have a control file (want to use ISL1 but that is an ELAND format). | ||
Line 139: | Line 139: | ||
And after "time java" (why time?) there is a flag that is sometimes given as -Xmx8g and sometimes as -Xmx2G - what is that about?'' | And after "time java" (why time?) there is a flag that is sometimes given as -Xmx8g and sometimes as -Xmx2G - what is that about?'' | ||
Ah, I think I missed the subfolder "classes" earlier. | |||
*'''[[User:Etchevers|Heather]] 03:30, 30 June 2009 (EDT)''': | *'''[[User:Etchevers|Heather]] 03:30, 30 June 2009 (EDT)''': | ||
<!-- ## Do not edit below this line unless you know what you are doing. ## --> | <!-- ## Do not edit below this line unless you know what you are doing. ## --> | ||
|} | |} |
Revision as of 00:32, 30 June 2009
Genetics of human eye development | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
Building FindPeaksI hate the way OWW will automatically log you out after a finite, arbitrary amount of time and NOT SAVE DRAFTS. Or at least I don't know where to find them. Make sure to apt-get install subversion first. U trunk/Changelog.txt U trunk/src/lib/analysisTools/Exon_Overlap.java U trunk/src/lib/analysisTools/Process_Exons.java U trunk/src/lib/Ensembl.java D trunk/src/projects/findFeatues A trunk/src/projects/findFeatures A trunk/src/projects/findFeatures/FindFeatures.java U trunk/src/projects/findPeaks/filewriters/PeakWriter.java U trunk/src/projects/findPeaks/PeakDataSetParent.java U trunk/src/projects/findPeaks/FPConstants.java U trunk/src/projects/findPeaks/FindPeaks.java U trunk/src/projects/findPeaks/objects/SaturationDataHolder.java U trunk/src/projects/findPeaks/objects/Parameters.java U trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java U trunk/src/projects/findPeaks/PeakDataSetChild.java U trunk/src/projects/findPeaks/FDR/MC_Simulation.java U trunk/src/projects/findPeaks/FDR/ApplyControl.java U trunk/src/fileUtilities/MaqPetToBedFormat.java U trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java U trunk/build.xml Checked out revision 1309.
calib-36.dat Documents hg18 maqview Pictures Templates Videos Desktop examples.desktop maq-0.7.1 Music Public trunk
Buildfile: build.xml does not exist! Build failed (Oops. One was forewarned.)
build.xml Changelog.txt classes jars lib src testdata
Buildfile: build.xml cleanfp: initfp: [mkdir] Created dir: /home/heather/trunk/jars/fp4 compile: [javac] Compiling 137 source files to /home/heather/trunk/classes FindPeaks: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar [delete] Deleting directory /home/heather/trunk/tmp SeparateReads: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar [delete] Deleting directory /home/heather/trunk/tmp SortFiles: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar [delete] Deleting directory /home/heather/trunk/tmp GenomeViewer: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar [delete] Deleting directory /home/heather/trunk/tmp ConvertToBed: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/ConvertToBed.jar [delete] Deleting directory /home/heather/trunk/tmp MaqPetToBed: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/MaqPetToBed.jar [delete] Deleting directory /home/heather/trunk/tmp buildfp: fptestdata: [copy] Copying 1 file to /home/heather/trunk/jars/fp4 changelog: [copy] Copying 1 file to /home/heather/trunk/jars fpsuite: BUILD SUCCESSFUL Total time: 7 seconds I've elided the few attempts where I messed up the pathnames, but here is the last one and I don't see why it can't find MaqPetToBedFormat, as the fileUtilities folder contains: BowtieToBedFormat.java MapHeaderInfo.java RegionToBed.java CombineFiles.java MaqPetToBedFormat.java SeparateReads.java ConvertToAce.java MaqToReadFormat.java SortFiles.java ConvertToBed.java RegionToAberations.java
Exception in thread "main" java.lang.NoClassDefFoundError: ~/trunk/src/fileUtilities/MaqPetToBedFormat Caused by: java.lang.ClassNotFoundException: .(~/).trunk.src.fileUtilities.MaqPetToBedFormat at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336) Could not find the main class: ~/trunk/src/fileUtilities/MaqPetToBedFormat. Program will exit. real 0m0.194s user 0m0.140s sys 0m0.020s Since I don't know what a class is, I can't fix the problem. I also wonder if I can use single-end tags rather than paired-end, and what it will do with the bridge flag if so. Then again, it seems like anything that hasn't been paired (everything in principle) will end up in :
On the Workflows page for FindPeaks, as a neophyte I would have found it really useful if Anthony added in the expected output. I will give it a try and see. I keep aborting this entry by accident - it's really frustrating. Anyhow, will try -qualityfilter 10 since recommended 10-20 and 30 was used in example. All parameter/flags are here and -saturation is particularly interesting. I also don't know whether the Monte Carlo or the Lander-Waterman false detection rate calculations are more adapted, when I don't have a control file (want to use ISL1 but that is an ELAND format). The LW FDR seems to more resemble the concept used in CisGenome. I suppose I could try one then the other? First the MC, then. -iterations 6 -auto_threshold 0.01 -eff_frac 0.7 (Uh-oh, what does <float> mean? Should I specify something after the -flag or not? Can't figure out what it would be for -auto_threshold - an example on the Workflows page is 0.01 -, perhaps automatic for -eff_frac then - no, specify as 0.7). And after "time java" (why time?) there is a flag that is sometimes given as -Xmx8g and sometimes as -Xmx2G - what is that about? Ah, I think I missed the subfolder "classes" earlier.
|