Smooth

Smooth can be used to reduce experimental noise over the chromosome profile. It uses a sliding window over the chromosome where the size of the window is either a number of clones or basepairs. If basepairs is choosen a clone is inside the window if more then half of the gene is inside. Each clone is fitted to the local median or mean in the window and the user can choose the impact by using a simple weight. The correction of each spot is exported as an extra float JE_smoothdiff.

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Changes

Revision 713

• Fixed problem with reading BASEfile spot sections, due to changes in BASEFileReader.
• Syncronized sample smooth.base​ configuration file and program code (mismatch in hidden section parameter).
• Change memory setting in run​ start script.