12 months ago by
Is sounds like you require IGV to visually indicate which RNASeq reads in a bam file are compatible with which transcript models that they overlap, and to what extent.
This is not a fully specified requirement, as it does not define "compatible" or "extent", and does not address issues such as:
- alternate splicing yielding overlapping transcript models
- over-lapping genes
Regardless, I believe IGV can not do this for you.
If you fully specify the requirement, you might be able to pre-compute "compatibility" for each read and add it as a user-defined custom FLAG in the sam/bam file, and then you can use IGV's popup-menu capability to color by the value of this attribute.
If you code in R, you may find the following abstraction and function useful: findCompatibleOverlaps
Depending on your application you will want to read: