LifeScope v2.5

[paolo.kunder]

Dear All,
is anyone using Lifescope for WT paired end analysis?

Reliable alignments can be obtained by setting a threshold on mapping quality, I want to know how to set the threshold? Is there any standard method for this setting?

LifeScope ask me to set a parameter ranging from 0 to 255, default one was set to 0, and my jobs ended up with all reads aligned with in average a bad quality mapping, now I would like to increase it..
any suggestions?

[seq_lover]

Copied from MAQ Documentation at http://maq.sourceforge.net/qual.shtml

What is Mapping Quality?

In a probabilistic view, each read alignment is an estimate of the true alignment and is therefore also a random variable. It can be wrong. The error probability scaled in the Phred is the mapping quality. If the mapping quality of a read alignment is $mQ, the probability $me that the alignment is wrong can be calculated with:

$me = 10 ** (-$mQ / 10.0);
Given 1000, for example, read alignments with mapping quality being 30, one of them will be wrong in average.

My views:

I use 20 for mapping. But I increase the stringency for tertiary analysis. For example, I only use aligned reads with mapping quality > 40 to call SNPs.

20 is less stringency i.e. 1 out of 100 alignment is a false positive.
40 is too stringent i.e. 1 out of 10000 alignment is a false positive.

Reading few sequencing paper related to your organism may help too.