Question: What causes this message in IGV?
gravatar for Y Tb
5.6 years ago by
Y Tb200
Y Tb200 wrote:

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 nmaes on this data, I can visulize 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 refence genome on tophat, also I provided the gene annotation file (.gtf) on tophat



sequencing rna-seq next-gen • 2.4k views
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Y Tb200
gravatar for Daniel Swan
5.6 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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.

ADD COMMENTlink written 5.6 years ago by Daniel Swan13k

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.

ADD REPLYlink written 5.6 years ago by Y Tb200

I think Charles has your answer!

ADD REPLYlink written 5.6 years ago by Daniel Swan13k
gravatar for Charles Warden
5.6 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

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).



ADD COMMENTlink written 5.6 years ago by Charles Warden7.8k
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