gene name and track missing

[Mary Kroetz]

I have been using IGV for the last few months and this week a problem
developed, which had not occurred earlier. If I am searching a
chromosomal region by using the chromosomal coordinates, I am no
longer able to see the gene names or a map of the exon/introns in the
gene track. However if I search the same region using the gene name
(instead of chromosomal coordinates), then I can see the gene names
and maps in the gene track.

This has never been a problem until Monday.

Is there someway that I can search using the chromosomal coordinates
and still be able to visualize the gene names and map?

Thank you for your help,
Mary

[James Robinson]

Mary,

What version of IGV are you using (do help > about to find out), and also what genome assembly are you viewing?

I'm not sure I understand you correctly, could you send a screenshot of what you see after you search?

Thanks

Jim

[Mary Kroetz]

Hi Jim,

I am using version 2.0.34 (1623). I am using the WS220 genome assembly for C. elegans.

The annotations for the gene tracks are no longer accurate, and sometimes not labeled. I have attached a ppt of screen shots from before the problem occurred and after.  It is for roughly the same chromosomal region.

I would appreciate any help to allow the gene tracks to return to how they were previously annotated, or to help locate what I might be doing to cause this new error.

Thanks you,
Mary

[James Robinson]

Mary,

That is curious, attached is what I see.

From your screenshot I infer you are using a Mac. Are you comfortable with a command terminal? If so try going to your "genomes" folder which is located at ~/.igv/genomes (~ means user home directory) and delete the "WS220.genome" file you find there. Then restart IGV and see if it looks the same. Deleting that file will force it to download a fresh copy, which it should be doing automatically.

Jim

[Mary Kroetz]

Hi Jim,

Thanks! That did help for the majority of genes.

I noticed that the WS220 annotation for T04A6.3 using IGV is not the same as the WS220 annotation for that gene on Wormbase.  If you don't mind could you see if this difference occurs on your end.

For me the IGV chromosomal position for T04A6.3 is ~III:7,606,661-7,610,648 and for Wormbase it is III:7,605,885-7,608,242.

Thanks,
Mary

[James Robinson]

We're using UCSC annotation for this assembly, could you see if the discrepancy is there?

Thanks

Jim

[Mary Kroetz]

Hi Jim,

UCSC has two annotations in that region.  The IGV annotation matches the RefSeq annotation but not the Ensembl prediction.

I've been following this particular gene, and the annotation of this gene has changed on IGV in the last few weeks from the Ensembl prediction to the RefSeq annotation.

Do you know why the annotation on IGV might have changed in the last few weeks?

Thanks again for your time and help,
Mary

[James Robinson]

Hi Mary,

The earlier WS220 annotation was contributed to us by email from a user, it did not come from an official source that we could attribute. We periodically update the annotations for all hosted genomes, but normally do not change sources as in this instance. I will add the Ensemble annoation for this assembly to the "File > Load from server" menu so you can optionally load it. If you need it before I can get to it you can download the track from UCSC and load it through the file menu. Many of their files just work, but the surest way to do it is use the table browser and output as "bed" format.

Apologies for the confusion,

Jim

[Mary Kroetz]

Thanks Jim,

The changes in the annotation make sense to me now. I'll try to upload the Ensemble annotation.

Best,
Mary

[Jim Robinson]

Hi,  I added the ensemble annotation to the "server" files for this genome.  You can load it by selecting  "File > Load from Server..." .

Jim

[Mary Kroetz]

Thank you!

[Kessara Chan]

Dear Jim, 

This post might be old but I do hope you are still here to help me find a solution to my problem. I am using IGV version 2.3.40 (48) and trying to find out different isoforms of a specifique gene from my RNAsequencing data. I would like to replace the refseq annotation to the ensembl prediction. Is it possible? If yes, could you provide me with a tutorial to do this? 

I am looking forward to hearing from you at your earliest convenience. 

Best regards, 

Kessara 

[Kessara Chan]

Also the genome I am using is Mouse (mm10)

[Jim Robinson]

Hi,

I just added this for you.  From the File menu select "Load from Server...",  then open the Annotations node and select the track.  Also, you can download the file from UCSC at this link, and load if from the File menu:  http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz.

Jim

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[Brenda Han]

I tried to load the Ensembl mm10 gene annotation track from server as Jim had described below, but it seems the link is broken (see attached screenshot). Eventually I managed to download the GTF file from Ensembl, sort --> index it for display on IGV, but I just thought you should be aware of this issue.

[James Robinson]

Thanks for letting us know

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