IGV colors entire BAM file as inversions

[SrCardgage]

I'm using the Integrative Genomics Viewer (IGV) to view the alignments achieved from TopHat.

I have four samples (and thus four BAM files). I've created indexes for all of them and each bam + index is in it's own directory. I am able to load the files just fine.

I have the reads colored by "insert size and pair orientation". According to this page http://www.broadinstitute.org/softwa...r_orientations, the entire second sample is comprised of inversions.

I've scrolled to many different positions on different chromosomes and all the reads are either blue or cyan (mostly blue). What is causing the program to understand the reads this way?

Thank you.

[SrCardgage]

typo explains it all

I figured out what the cause was. I mistyped the tophat command and used only the first sequence file for both the first and second sequence files.

I'm surprised it made it this far through the pipeline!