With the release of PeakTrace 6.40 we have updated the setting for the free version of PeakTrace (PeakTrace Online) to make optimal use of the improvements incorporated into this version. The new settings are now
-t abi -ft 300 -c -40 -wq 12 20 -xb 7 -cb yes -bc pk -ts no -xs 1000 2 -sm 700
These values correspond to the Auto PeakTrace and Auto PeakTrace RP Option settings:
- fuse trace at base: 300
- good base improvement: −40 bases
- q average trim: 12 threshold; 20 base window
- clean baseline: yes
- extra baseline: 7
- basecaller: peaktrace/kb (PeakTrace Basecalling with KB fallback)
- trim 3’ end only: yes
- extra smoothing: level 2; start base 1000
- skip short/pcr base: 700
These settings are not suitable if you are trying to detect polymorphic sites (i.e. mixed peaks). For this you need to use a mixed peak threshold above the default 0.
The PeakTrace default values are usually the best place to start, but you should always trial the various options to find what works best for your needs. If you would like further advice on the best settings to use with your sequencing data, please don’t hesitate to contact us @ {This email is obscured. Your must have javascript enabled to see it}.