Changes between Version 12 and Version 13 of SOPs/chip_seq_peaks

Timestamp:

05/20/14 15:02:26 (11 years ago)

Author:

ibarrasa

Comment:

--

SOPs/chip_seq_peaks

@@ -64 +64 @@
   * --mfold=MFOLD      Select the regions within MFOLD range of high-confidence enrichment ratio against background to build model. The regions must be lower than upper limit, and higher than the lower limit. DEFAULT:10,30
   * -g GSIZE  Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs
-  * --keep-dup=1   Controls the MACS behavior towards duplicate tags at the exact same location.  DEFAULT: 1 in MACS 1.4; auto in MACS2.   
+  * --keep-dup=1   Controls the MACS behavior towards duplicate tags at the exact same location.  DEFAULT: 1 in both MACS 1.4 and MACS2.   
   * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. by default it means shifting size = 100.                      
   * --shiftsize The arbitrary shift size in bp. When nomodel is true, MACS will use this value as 1/2 of fragment size. DEFAULT: 100.