Etchevers:Notebook/STRA6 in eye development/2009/07/20

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 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |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

*Info:   Reads used: 103765 *Info:   Reads used: 161243 *Info:   Linear Regresion: Total:	12 *Info:   Linear Regresion: Used:	0 *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.'''
 * 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
 * Version: Initializing class PeakStats                        $Revision: 1335 $
 * Version: Initializing class Histogram                        $Revision: 1197 $
 * Info:   Current chromosome : chr17
 * Version: Initializing class ApplyCompare                     $Revision: 1332 $
 * Version: Initializing class LinearRegressionPerpendicular    $Revision: 1285 $
 * 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.
 * Heather 03:05, 21 July 2009 (EDT):


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