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Old 09-28-2009, 01:05 PM   #191
kmcarr
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Location: USA, Midwest

Join Date: May 2008
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Quote:
Originally Posted by apfejes View Post
Hi ka123$,
I should also mention that the "-aligner" format used sets the format and some of the behaviours of FindPeaks. If you've selected "-aligner eland", then FindPeaks expects the files you provide to be in the Eland format. I don't know what format Gerald uses, but I'm certain it's not the same as the output from the Eland aligner.
Anthony,

Actually the GERALD output is the appropriate place to look. GERALD.pl is a wrapper script which (among other things) calls the Eland aligner. The output from Eland is then placed in the "GERALD_<DD-MM-YYYY>_<USERNAME>" folder. Included in that output is the s_N_eland_extended.txt, s_N_eland_multi.txt, s_N_export.txt and s_N_sorted.txt. As you stated the s_N_sorted.txt file should be able to be used in FindPeaks directly. (I've never done it myself so I can't speak from experience.)

After looking at your link above I think the problem may be that Kal needs to specify elandext as the "-aligner" parameter. While the program is still called the "Eland" the standard "eland" invocation is essentially deprecated. The program is now almost always invoked (through GERALD) using "eland_extended".

Last edited by kmcarr; 09-28-2009 at 01:11 PM. Reason: Add bit about eland_extended
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