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Old 09-28-2009, 01:05 PM   #191
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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.

Actually the GERALD output is the appropriate place to look. 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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