periodicity in decay of quality

[yoyoq]

is it normal for the SOLiD quality to decay in a 5 base position
repeating pattern?
the boxplot image is attached.
this happened for multiple runs

thanks
jpd

[OneManArmy]

Yes, this is normal chemistry of the SOLiD system - there in increased noise in the later ligation cycles for each primer.

[nilshomer]

is it normal for the SOLiD quality to decay in a 5 base position
repeating pattern?
the boxplot image is attached.
this happened for multiple runs

thanks
jpd

The chemistry measures two bases in this order:
1. adaptor & b1 (base one)
2. b5 & b6
3. b10 & b11
4. b15 & b16
5. b20 & b21
6. b1 & b2
7. b6 & b7
8. b11 & b12
9. b16 & b17
10. b21 & b22
11 ....

so you see that since measurements skips every five bases, until it reaches the end, where it starts at the beginning but one base forward. So you can see that the ligation cycles are correlated (try reordering the graph with the ordering above ).

[ECO]

[nilshomer]

Fancy pictures...

[yoyoq]

wow crystal clear, thanks.
would you say our data run looks low in quality?
we are having trouble getting clean output