Do you have any examples of how GenomeBrowse displays inversions or rearrangements (or any discordant read pairs)?
Our support for structural variations is currently fairly limited, but here is what we have so far. Note that these require the "Stack Paired-end" option to be enabled. Click the gear menu in the upper left of the pileup plot, and then click "Stack Paired-end".
Nearby alignments from the same read pair are connected with a thin gray line.
If a mated pair is separated by more than 1000bp, then they will not be connected with a line. Instead, they will have a small arrow pointing in the direction of their mate. Clicking on the alignment will show a detailed report in the data console which includes more information on the mate. This 1000bp limit exists mostly for technical reasons (pileups get very large and unwieldy with lots of long mated pairs). However, future versions of GenomeBrowse might allow the 1000bp limit to be user-modified.
If an alignment's mate is on another chromosome, then a double-headed arrow is drawn pointing in the direction of the mate.
There's been a lot of interest among our users regarding structural rearrangements, so we welcome any suggestions for improvement you might have!
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2012-10-01 11:19:26 -0600
Seen: 8,412 times
Last updated: Oct 03 '12