As the question declares I want to know how pacbio quality is calculated?
If I am using the SMRT portal for example RS_Subreads.1
In the filtering process It will give me this values
SFilter v1 Minimum Subread Length 50 Minimum Polymerase Read Quality 75 Minimum Polymerase Read Length 50
I can change It but how it is calculated?
I know that there is two basic steps the Basic analysis step which begins with movie -> puls -> kinetic measures -> and at last bases
the second step which is called secondary analysis, using the smrt portal which I can change the numbers in each algorithm but how it is related to the main sequences?