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  • pair reads visualization

    Hi all,

    is there a way in IGV (or other viewer) to visualize the pair reads, displaying each pair couple in a single line? I want to see how the two reads of each pair are far/close to each other. By default, after I load the bam file, each read of a pair is aligned to the reference, but the two reads of the same pair are not on the same line. So, with thousands of reads, I can't understand how the reads of the same pair couple are mapped relatively to each other..

  • #2
    "Select View as pairs from the right-click menu to display pairs together with a line joining the ends as shown in the image below."
    If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.
    Last edited by blancha; 11-02-2015, 07:33 PM.

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