Etchevers:Notebook/STRA6 in eye development/2009/07/20: Difference between revisions

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==Chr 17 comparison==
==Chr 17 comparison==
Launched the following comparisons between Chr 17 RAX and PAX6, which gave a fair number of peaks each in the Fasteris analysis. Many fewer were found not to be common between the two, and again there was no filtering (bold).
Launched the following comparisons between Chr 17 RAX and PAX6, which gave a fair number of peaks each in the Fasteris analysis. Many fewer were found not to be common between the two, and again there was no filtering (bold).
'''time java -Xms2G -Xmx11G -jar ~/trunk/jars/fp4/FindPeaks.jar -name PAX6-RAX-FP-Chr17 -input /home/oeil/Documents/Fasteris_7_2009/GDZ5_PAX6_bed/PAX6_Chr17.bed -output /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17 -aligner bed -dist_type 1 200 -minimum 20 -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr17.bed -alpha 0.05'''


*Version: Initializing class Parameters                        $Revision: 1298 $
*Version: Initializing class Parameters                        $Revision: 1298 $

Revision as of 00:09, 21 July 2009

Genetics of human eye development <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Chr 17 comparison

Launched the following comparisons between Chr 17 RAX and PAX6, which gave a fair number of peaks each in the Fasteris analysis. Many fewer were found not to be common between the two, and again there was no filtering (bold).

time java -Xms2G -Xmx11G -jar ~/trunk/jars/fp4/FindPeaks.jar -name PAX6-RAX-FP-Chr17 -input /home/oeil/Documents/Fasteris_7_2009/GDZ5_PAX6_bed/PAX6_Chr17.bed -output /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17 -aligner bed -dist_type 1 200 -minimum 20 -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr17.bed -alpha 0.05

  • Version: Initializing class Parameters $Revision: 1298 $
  • Info: * MC simulation  : Off
  • Info: * Chr name prepend  : none
  • Info: * Min. reported pk ht  : 20
  • Info: * Minimum ht to process: Off
  • Info: * Lander-Waterman FDR  : Off
  • Info: * Output Sequence  : Off
  • Info: * Output directory  : /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/
  • Info: * Control files in use : Off
  • Info: * Compare files in use : On
  • Info: * Peak ht transform  : false
  • Info: * Compare window size  : 100
  • Info: * Auto-threshold  : Off
  • Info: * Filter on PET flags  : Off
  • Info: * Maximum PET frag size: Off
  • Info: * Aligner  : bed
  • Info: * Triangle dist.  : 100 low
  • Info: * Triangle dist.  : 200 median
  • Info: * Triangle dist.  : 300 high
  • Info: * One file per chr.  : Off
  • Info: * Naming files as  : PAX6-RAX-FP-Chr17
  • Info: * Sub-peaks  : Off
  • Info: * Trim  : Off
  • Info: * Saturation Analysis  : Off
  • Info: * Compare alpha value  : 0.05 (Confidence Interval: 95.0)
  • Info: * Histogram length  : 30
  • Info: * Histogram precision  : 1
  • Info: * Peaks File Header  : On
  • Info: * Bedgraph/Wigfile  : wig file
  • Info: * R mode  : Off
  • Info: * Filter Duplicates  : Off
  • Info: * Filter quality  : Off
  • Version: Initializing class PeakWriter $Revision: 1299 $
  • Version: Initializing class Generic_AlignRead_Iterator $Revision: 1318 $
  • Version: Initializing class BedIterator $Revision: 1317 $
  • Info: Running Peak Processor
  • Version: Initializing class PeakDataSet Peak Locator $Revision: 1335 $
  • Version: Initializing class PeakStore $Revision: 1335 $
  • Version: Initializing class MapStore $Revision: 1335 $
  • Info: Current chromosome : chr17

*Info: Reads used: 103765

  • Version: Initializing class PeakStats $Revision: 1335 $
  • Version: Initializing class Histogram $Revision: 1197 $
  • Info: Current chromosome : chr17

*Info: Reads used: 161243

  • Version: Initializing class ApplyCompare $Revision: 1332 $

*Info: Linear Regresion: Total: 12 *Info: Linear Regresion: Used: 0

  • Version: Initializing class LinearRegressionPerpendicular $Revision: 1285 $

*Warning: Can't run a Linear Regression calculation with zero points. *Warning: Can not apply filter. A valid slope was not obtained from the analysis.

  • Info: Linear Regresion: Remaining: 12
  • Version: Initializing class RegionWriter $Revision: 1229 $
  • Info: writing to : /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17.regions
  • Version: Initializing class Wigwriter $Revision: 1329 $
  • Info: writing sample to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17_filtered_sample.wig.gz
  • Info: writing comtrol to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17_filtered_control.wig.gz
  • Info: writing to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17.wig.gz

The end of the file was marked "Killed" and the time was at some 647 minutes in real time, just under 10 for the CPU and something like 6 for the user (or vice-versa; they closed the terminal window before I could copy it in). We really need more memory but it will only accommodate to 8 Mb.

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