5.6 years ago by
1) You can define a custom reference from any .fasta file (which, if you want can be transcripts rather than chromosomes, but I wouldn't typically recommend that):
(see creating a .genome file)
2) I typically load special tracks as .bed files, but I think the .gtf files will also work:
However, the .gtf file has to specify the annotations with respect to the reference that you actually aligned against. For example, if you align against RefSeq transcripts (with one entry per transcript in the reference), then it won't be be helpful to have a .gtf file specifying annotations for hg19. However, it sounds like loading a .gtf file for mm9 should be OK in your case
3) It is a roundabout solution, but you can first query the gene in the UCSC genome browser and then view your data in IGV based upon genomic coordinates instead of gene name (for example, I don't know if you can search for text within the additional tracks or if they are just useful for visualization).