Re: [Pairoscope-help] grey bar in plot

[Dave L. <dl...@ge...>]

Dear Yaping,
     You are correct. It is possible to get grey lines if the 
orientation is correct, but the aligner has marked it as not being a 
proper pair. To answer your second question, if both mates are mapped 
within the region then an arc is drawn between them. The long bars that 
you see are a result of reads being mapped right next to (or 
overlapping) with their mates. In this case, the arc appears as a 
straight line due to the proximity of the two reads.

Hope that helps,

Dave

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Human Genomics
The Genome Institute
Washington University School of Medicine
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