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Old 09-28-2009, 10:33 AM   #189
Ka123$
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Location: MD

Join Date: Jul 2009
Posts: 27
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Thanks to both kmcarr and apfejes !
I did belive that GERALD generates the Eland format files. But when I used GERALD files to perform a separate reads according to findpeaks and I used ELAND as an aligner name it gave me an error saying that it was a wrong aligner name.......hence needed a confirmation as to what I thought was actually the correct thing or not.....
I dont know why it said that?
Did I have to use GERALD.fa or the export file? not sure....

Why I needed to use GERALD instead of aligned files?
Reason being,when I used the findpeaks tool to perform a conversion of my aligned files to wig files , I would need to go through the separate and sort files..... When I perform separate files using bowtie aligned files, I get just one gi|......|.......|.part.bowtie.gz which contains the contigs with each contig having the name gi|.....|.....| etc along with their position w.r.t the reference.

Why did I get only one gi|........file although I have separated it? if I sorted this either a gz or gunzipped I get memory error
as whenever I used sort files on this I get memory heap error: at 2300000 lines read.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.lang.String.substring(Unknown Source)
at java.lang.String.subSequence(Unknown Source)
at java.util.regex.Pattern.split(Unknown Source)
at java.lang.String.split(Unknown Source)
at java.lang.String.split(Unknown Source)
at src.lib.ioInterfaces.BowtieIterator.next(BowtieIterator.java:145)
at src.lib.ioInterfaces.BowtieIterator.next(BowtieIterator.java:20)
at src.lib.ioInterfaces.Generic_AlignRead_Iterator.hasNext(Generic_AlignRead_Iterator.java:103)
at src.fileUtilities.SortFiles.main(SortFiles.java:79)

although I use -Xmx2G........


So we thought we could use GERALD to separate into indiv chr and then sort on each indv chr instead?????

ANy suggestions?
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