I very much like the IGB tools and its features. While I have been able to make a good use of it, I have been facing a problem and can't seem to find a solution how much I try. I am trying to view the aligned tophat output (mapped.bam and junction files from aligned RNAseq data on the reference A. lyrata genome. When I load the lyrata genome on the IGB browser I can see the genome coordinate and the TAIRmRNA database (the annotated .gff file). But, after I upload a mapped.bam and junction file I am not able to see the alignment (aligned reads) with the reference and the annotation.
But, I figured that the mapped.bam and junction creates its own set of scaffold at the bottom of the default set of scaffold (one to one copy with default, but not sure why?). So, if I select a scaffold that the mapped.bam file has created I am able to see the mapped reads and the junctions but now cannot see the co-ordinate bases and the annotations. However, with A. thaliana genome there is no such problem with viewing the mapped output and junctions from RNAseq data along with genome coordinates and bases, TAIR10 mRNA database and several other databases from other labs.
Also, I see that updated version of phytozome data is available (V10.2). Is the data for A. lyrata available on IGB browser (V7) the same as V10.2?