What causes this message in IGV?

Question

[Y Tb]

I am trying to visulize rna-seq mapped data for mouse from Tophat results (accepted_hits.bam file). I used mm9 as a reference genome in IGV. When I looked for specific names on this data, I can visualize some of them but the others not shown and IGV gave me the following message Cannot find feature or locus: Gm9951

BTW: I used the same reference genome on tophat, also I provided the gene annotation file (.gtf) on tophat

Answer 1

[User 59]

Just because you've provided those to TopHat doesn't mean they will bear any relation to what you can search on in IGV - the annotations are not linked in that way. You will probably want to load perhaps the Ensembl gene track from the IGV menus. In my experience the gene models in IGV are not the best set of annotations.

[Y Tb]

Dear Daniel,

Thanks for your respond. Is there any way to use the same reference genome and same release or gtf file that I used in Tophat directly on IGV instead of using the defaults one on it.

[User 59]

I think Charles has your answer!

Answer 2

[Charles Warden]

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):

http://www.broadinstitute.org/igv/LoadGenome

(see creating a .genome file)

2) I typically load special tracks as .bed files, but I think the .gtf files will also work:

http://www.broadinstitute.org/igv/GFF

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).