splice junction reads

[Musa Hassan]

Hi,
I am trying to view reads aligning to splice junctions in igv. I've used the view->preferences and set to view splice junction aligning reads, but I still can't see a demarcation for these reads. I am doing this wrong?
while at it, does IGV have a way to view reads aligning to different transcript variants?
Regards,

[Jim Robinson]

I assume you've loaded a bam and zoomed in sufficently far to see the
reads. By default this is 30 KB, but for rna-seq data you can safely
set this to a larger value (200kb or more). You do this in the
preferences panel, its the first field.

Could you post a screenshot of what you are seeing, or email it to
igv-...@broadinstitute.org?

Jim

[Musa Hassan]

Hi,
Is there a way to display paired-reads? I guess I've seen this feature before in IGV but can't figure it out in my time of need.

On 1 February 2012 12:44, James Robinson via RT <igv-...@broadinstitute.org> wrote:

 Well, first you have to have used an aligner that can map reads across
junctions.  Assuming you have done that,  the reads themselves will be
broken into blocks separated by thin lines representing the junctions.
The attached screenshot shows both reads and the "junction" track for
some RNA-seq data.

Jim


> <URL: https://rt.broadinstitute.org/Ticket/Display.html?id=145253>
>

> I guess my question now is, from the view, how can I tell where the
> junction is?
>
> On 1 February 2012 12:06, James Robinson via RT<igv-...@broadinstitute.org
>> wrote:

[James Robinson]

Hi,  

I'm not precisely sure what you are looking to do,  but try right-clicking and select "view as pairs".   This will only work if the pair information is encoded in the BAM file.

Jim