Etchevers:Notebook/STRA6 in eye development/2009/09/02: Difference between revisions
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Yesterday's installation attempt was from "Révision 1496 extraite". | Yesterday's installation attempt was from "Révision 1496 extraite". | ||
Today's yields "Révision 1516" instead - so let's see how progress is. First | Today's yields "Révision 1516" instead - so let's see how progress is. First difference - | ||
"Compiling 157 source files to /home/heather/trunk/classes" | |||
then | then | ||
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Now load up the Fasteris data and try something out. | Now load up the Fasteris data and try something out. | ||
Example updated by Andrew on his workflows page: | [http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=WorkFlows#Example_using_Eland_aligner: Example updated by Andrew on his workflows page:] | ||
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time java -Xmx2G -jar FindPeaks.jar -name test -input /path/to/*.part.eland.gz -output /output_path/ \ | ''time java -Xmx2G -jar FindPeaks.jar -name test -input /path/to/*.part.eland.gz -output /output_path/ \ | ||
-aligner eland -one_per -dist_type 1 200'' | -aligner eland -one_per -dist_type 1 200'' | ||
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* to prevent singleton mapping reads from appearing, you can use a minimum height cutoff (-minimum 2) | * to prevent singleton mapping reads from appearing, you can use a minimum height cutoff (-minimum 2) | ||
* '''if histograms are not required, they can be turned off by setting histogram size to 1. (-hist_size 1)''' | * '''if histograms are not required, they can be turned off by setting histogram size to 1. (-hist_size 1)''' | ||
* '''if you know the exact size of each read, you can use a fixed length extension (-dist_type 0 <size>)''' or use the size of the sequence itself (-dist_type 3) | * '''if you know the exact size of each read, you can use a fixed length extension (-dist_type 0 <size>)''' \ | ||
'''or use the size of the sequence itself (-dist_type 3)''' | |||
* multiple peaks can be identified in complex regions for peaks files (-subpeaks <parameter>) [not for me] | * multiple peaks can be identified in complex regions for peaks files (-subpeaks <parameter>) [not for me] | ||
Revision as of 01:22, 2 September 2009
 Genetics of human eye development
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New release Sept 1st of FP 4.0.5Yesterday's installation attempt was from "Révision 1496 extraite". Today's yields "Révision 1516" instead - so let's see how progress is. First difference - "Compiling 157 source files to /home/heather/trunk/classes" then buildall: BUILD SUCCESSFUL Total time: 6 seconds Yay! Now load up the Fasteris data and try something out. Example updated by Andrew on his workflows page: time java -Xmx2G -jar FindPeaks.jar -name test -input /path/to/*.part.eland.gz -output /output_path/ \ -aligner eland -one_per -dist_type 1 200 ' You may need to add the optional "-prepend chr" tag, if your chromosome names/numbers do not contain this prefix.' Some simple parameter changes of interest: * to prevent singleton mapping reads from appearing, you can use a minimum height cutoff (-minimum 2)
* if histograms are not required, they can be turned off by setting histogram size to 1. (-hist_size 1)
* if you know the exact size of each read, you can use a fixed length extension (-dist_type 0 <size>) \
or use the size of the sequence itself (-dist_type 3)
* multiple peaks can be identified in complex regions for peaks files (-subpeaks <parameter>) [not for me]
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