Macs 1.4.0 (note that 1.4.1 is the current version) has a number of changes and bugfixes. See http://liulab.dfci.harvard.edu/MACS/ChangeLog.html for the list.
Among them the handling of duplicate reads, changes in how samples are scaled etc, all could affect the output.
Personally, I'd go with the newer version. Adjust your mfold (the old one had x >= 32, the new one 10 <= x <= 30), and you should get comparable results for strong peaks.
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MACS version 1.3.0 versus MACS version 1.4.0
i have tried calling peaks by both the versions of MACS. incidentally i got a model with 1.3.7 but did not get any model with 1.4.0 a warning instead
(too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, please use --nomodel and --shiftsize 100 instead.)
the output for peak calling is also different with the two versions. Now my question is: Is it better to continue using the older version? does anybody knows the advantages of the newer version as compared to the older version? galaxy still uses version 1.3.7. what is the most commonly preferred version?
Thanks in advance
Neetu
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