How IGV displays multiple mapping reads

[Yung-Chih Lai]

Hi,

 

I understand how unique mapping reads were displayed. However, I don't know understand how multiple mapping reads were displayed in the IGV. For example, if one read was mapped on 3 regions, it will be appeared on the 3 regions in IGV? Or IGV will remove reads mapped on multiple locations? Many thanks.

 

Gary

[Jim Robinson]

Hi,  multiply mapped reads are not removed by default, but if the aligner has properly tagged the reads as "primary" and "secondary" you can filter the secondary alignments.   Select "View > Preferences > Alignments tab" and check the "Filter secondary alignments" box.

[He Fang]

Hi,

I have a similar question. I don't check the 'Filter secondary alignment" box so as you mentioned the reads tagged as 'secondary' are also displayed. I can see the reads are labeled as 'secondary=Yes' when I check certain region. My question is how these multiple mapping reads are displayed genome wide? For example, if read 'A' is be mapped to 'b', 'c' and 'd' regions, will 'A' be displayed only in one of these regions or it will show up in all three regions?

Thank you very much

[James Robinson]

It will show in all regions if there are alignments in all regions.   IGV does not display reads, it displays alignments.   So it will display whatever your aligner writes to the file.

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