Question: IGV SNP glyph question
0
gravatar for mark.rose
4 weeks ago by
mark.rose10
United States
mark.rose10 wrote:

Hi All

I'm visualizing an alignment of Illumina paired end data in IGV. Some of the SNPs observed are rendered as glyphs consisting of a solid bar where as others appear as a bar with a gap in the middle. Looking at the alignment it appears that the gapped bar occurs where read1 and read2 do not agree but I am not positive of this. Does anyone know if this is correct, and, if not, what is the true explanation.

Thanks much

Mark

igv snp • 138 views
ADD COMMENTlink modified 29 days ago by finswimmer2.1k • written 4 weeks ago by mark.rose10

Hello mark,

could you please post a screenshot of IGV?

fin swimmer

ADD REPLYlink written 4 weeks ago by finswimmer2.1k

enter image description here

This is with v 2.4.10 which has some advanced graphics for viewing paired read overlays

ADD REPLYlink modified 29 days ago by Ram15k • written 29 days ago by mark.rose10

@mark please use the directions here: How to add images to a Biostars post

ADD REPLYlink written 29 days ago by genomax48k

enter image description here

ADD REPLYlink modified 29 days ago by Ram15k • written 29 days ago by mark.rose10

Dont know why its not visible in the post but if you right click either of these links the you can open the image

Ah, wait. Now its visible

ADD REPLYlink modified 29 days ago • written 29 days ago by mark.rose10

Did you read my comment here? C: IGV SNP glyph question

ADD REPLYlink written 29 days ago by Ram15k

Note the darker arrowhead of read 2's overlap at position 15

ADD REPLYlink written 29 days ago by mark.rose10

Both of the links I sent (imgur and cubupload) open when I right click on them but not within the post itself

ADD REPLYlink modified 29 days ago by Ram15k • written 29 days ago by mark.rose10

I think you picked the wrong link. The link you used is part of cubeupload's HTML embed code. It's used in the <a href= part and not the <img src= part, (it is not a direct link to the image file, just to a webpage). If you see the How-to post, the direct link, highlighted in blue, stars with i.cubeupload. That link will work, not the one you used.

ADD REPLYlink modified 29 days ago • written 29 days ago by Ram15k

imgur works too, you just gotta use the direct link to the image (https://i.imgur.com/x77Z27m.png) and not the website URL from the browser address bar (https://imgur.com/a/ka2N8xB).

ADD REPLYlink modified 29 days ago • written 29 days ago by Ram15k
0
gravatar for finswimmer
29 days ago by
finswimmer2.1k
Germany
finswimmer2.1k wrote:

Looking at the alignment it appears that the gapped bar occurs where read1 and read2 do not agree but I am not positive of this.

You use the option "View as pairs". The region where you have this "gap" is the region where the read overlaps. The horizontal line isn't just where the SNPs are located.

fin swimmer

ADD COMMENTlink written 29 days ago by finswimmer2.1k

Not sure of your point. Yes, I am viewing them here as pairs. When I view them singly, they are solid bars, where the blue ones (in this case) are present only in one of the two overlapping reads. For other SNPs (viewed as pairs, not shown) that occur in overlapping regions but are called in both reads, the bar is solid.

ADD REPLYlink written 28 days ago by mark.rose10
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