Hello all,
In IGV, reads with a mapping quality = 0 are displayed in white while reads
with a positive mapping quality are displayed in grey (at least for the bam
file I am trying to analyze).
From what I could deduce from the information displayed when I hover over a read, I thought that white reads would be the ones mapping at several locations on the reference genome while grey reads would be the ones with a unique mapping location. However, I just found some grey reads with XA tags, which in my case, mean that they map to 3 different locations on the genome...
AAAAAAAArrrgh!!
I don't understand what I'm doing, I guess...
Could anyone explain to an idiot like me, how this works? What is the
mapping quality then? How can I determine which are the reads with a unique
target in the genome?
Thank you very much in advance for your help
-a-
In IGV, reads with a mapping quality = 0 are displayed in white while reads
with a positive mapping quality are displayed in grey (at least for the bam
file I am trying to analyze).
From what I could deduce from the information displayed when I hover over a read, I thought that white reads would be the ones mapping at several locations on the reference genome while grey reads would be the ones with a unique mapping location. However, I just found some grey reads with XA tags, which in my case, mean that they map to 3 different locations on the genome...
AAAAAAAArrrgh!!
I don't understand what I'm doing, I guess...
Could anyone explain to an idiot like me, how this works? What is the
mapping quality then? How can I determine which are the reads with a unique
target in the genome?
Thank you very much in advance for your help
-a-
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