[doron]

Adding attachments to last post

I hope this time it will attach...

[Joker!sAce]

Hey, I'm using IGV too. I'm just starting on it and I like it, It's a great tool.

[crisant]

Hi Jim, I started to use IGV and seems to be fantastic. I have maize RNAseq and sorghum RNAseq. For the first I used the built-in genome and was nice, no porblem with that. I would like now to mapp the sorghum reads and was nice too, but I can't see the genes in the lower window (I see the reads in the upper window). Let me explain what I did: I imported the sorghum genome in fasta and in the "gene file" I choosed a GGF file (Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff), but nothing appeared in the lower window. What I am doing wrong? Thanks for any help.

[Jim Robinson]

Hi,

This problem is usually caused by a mismatch in the sequence (chromosome) names between the gff and fasta files. The fix is to either rename the sequence names in one of the files (usually the GFF), or create an alias table as described below (look at the bottom of the page).

http://www.broadinstitute.org/software/igv/LoadData

-- Jim

[crisant]

Thanks Jim, resolved.
Regards

[ndeshpan]

Is the IGVViewer site down?

[Jim Robinson]

It looks like all the Broad servers were down for a short period, they are back up now. Sorry for the inconvenience.

-- Jim

[dphansti]

Hi all,

I am trying to use IGV to visualize genomic differences between yeast strains. Right now I am having trouble viewing data from just a single strain. The aligned data (using BWA) can be loaded and visualized in IGV with no problem. However, when i use samtools and bcf tools to make a pileup and then a vcf file I get an error when i try to the load the vcf file into IGV. The error says...

"Error loading features: Unable to find required field GT for the record; we don't yet support a missing GT field, at line number #### Unload track test.vcf?"

I tried loading a vcf file from the 1000 genomes project and it worked fine.

Any suggestions? FYI, I am totally new to this field so go slow.

[Jim Robinson]

Hi,
The error message indicates that you are missing a GT field for one or more records. This field is currently required by the code we use to read VCF files (taken from the GATK). I'll update this thread when this is resolved, apologies for the inconvenience.

[nilshomer]

Use "bcftools view -g" to call genotypes, which gives the GT field.

[dphansti]

That worked. Thank you both.

[Alexander Tchourbanov]

Dear Jim,

I think the IGV is fantastic tool, thanks for developing it. I find several ways to improve the presentation. To my understanding it does not allow quick navigation by rolling the mouse and dragging the ruler. If implemented, this would be significant advantage over the existing online genome browsers, that have more static means of control. I have also found that the reference genome annotation may benefit from more colorful attributes, to delineate CDS from UTRs. An example display could be found here. Is there way to display multiple gene isoforms for human reference genome, like in case of CD44?

Thanks,

Alexander

[Jim Robinson]

Hi Alexander,

Thank you for the suggestions. I'm afraid I don't understand exactly what you mean by "rolling the mouse and dragging the ruler". You can click and drag the view left and right as in google maps, drag the red rectangular bar, click on the cytoband, and use the keys (arrow, home end). There are also several ways to zoom. So please elaborate on specifics.

With respect to multiple isoforms, yes, right click on the track and select "Expand" or "Squished".

Best,

Jim

[Alexander Tchourbanov]

Jim,

Thanks for quick response. Now I see how the coordinates could be changed by dragging and how isoforms could be displayed. What I meant is that central wheel on he mouse that can control the zoom on the Google maps when scrolling.

Sincerely,

Alexander

[Jim Robinson]

Ah yes, that would be useful. But the scroll wheel is also used for scrolling vertically through tracks. Perhaps this could be a user preference.

Jim