visualizing split reads / secondary alignments in IGV

[Nasir Amra]

I am trying e the to visualize split reads of fusion genes using IGV ( if it is possible). I can imagine having the aligner spit out supplementary alignments in the sam/bam ( I'm using a customized transcriptome consisting only of mRNA of a few genes as reference genome), but it is not clear to me how to use igv to visualize the split reads. I can manually setup up a multiview between the two fusion gene partners, but I can't figure out how to color code or label primary alignmnet read and secondary alignment in the mutli-view of the two fusion partner genes. Is there any tutorial on how to do this? If it even feasible?

Cheers,

Nasir

[James Robinson]

If the split alignments are on different sequences, which it sounds like they are, you (currently) cannot link them visually.  You can select individual alignments which will highlight alignments with the same read name.  On a mac this is "command-click", I don't recall what the modifier key is on Windows but probably "FN".