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Old 09-30-2009, 03:31 PM   #196
Ka123$
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Location: MD

Join Date: Jul 2009
Posts: 27
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Hi Anthony,
so here is what I am doing. We have decided to stick with the GERALD files to convert it to wig.......(PI's order !)
I checked for unaligned files and none were there.
I have a .export file with a s_#_export.txt
java -Xmx2G -jar SeparateReads.jar elandext 7_XXXXXX_GERALD-YYYY-MM-DD.export G_sep_7
Version: Initializing class SeparateReads $Revision: 1082 $
Version: Initializing class Generic_AlignRead_Iterator $Revision: 1318 $
Version: Initializing class Log_Buffer $Revision: 1145 $
Version: Initializing class ElandExtIterator $Revision: 832 $
Exception in thread "main" java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at src.lib.ioInterfaces.ElandExtIterator.next(ElandExtIterator.java:180)
at src.lib.ioInterfaces.ElandExtIterator.next(ElandExtIterator.java:20)
at src.lib.ioInterfaces.Generic_AlignRead_Iterator.hasNext(Generic_AlignRead_Iterator.java:103)
at src.fileUtilities.SeparateReads.main(SeparateReads.java:69)
^[[A

It looks like that GERALD gives out a .txt file . How can I specify what type of aligner is gerald? If I did elandext or eland_extended it does not work......

is there a way to directly convert a .txt from solexa export files to .wig in findpeaks?
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