Entering edit mode
7.3 years ago
nuketbilgen ▴ 40
I am new in the next generation analysis. I have 3 whole gene sequences.
I have several questions,
- How should I decide mapQuality filter value? Most of my reads has 60, but when I use 60 to filter my reads I lose approximately 3kb in one gene.
- Is it possible to give different MapQ values for different chromosome with bamtools? I am planning to use in one gene mapQuality">=20" and in the other two genes mapQuality">=60".