IGV coverage window

[Olivia]

Hi,

I'm looking for a very simple information, but can't manage to find
it.
I'm using IGV 2.0.6(860).
In the coverage track that appears above the track containing the
aligned reads of my bam file, some values are shown between brackets
(for example [0 - 352]). I just would like to know what they mean
exactly. Is this the coverage for a region around the position ? How
wide is this region and how is it defined? Can I modify it?

Thanks for your help.

Olivia

[Jacob Silterra]

Hi Olivia,

Details on the coverage track are available at https://www.broadinstitute.org/software/igv/AlignmentData.
The numbers in brackets are the range on the bar graph. The number plotted is the average coverage of a region, which will vary depending on the zoom level you are looking at. The track can be created with the igvtools "count" command, see http://www.broadinstitute.org/software/igv/igvtools_commandline for details. By default, the coverage is averaged over 25 bp. This is a command line parameter, so you can create files with different region sizes and windowing functions (see igvtools_commandline link above). IGV will look for a tdf file with the same name as the bam file you are loading to use as a coverage track.

-Jacob

--
Jacob Silterra
Software Engineer
Broad Institute

[Olivia]

Thank you for your answer.

The numbers in brackets don't vary when I change the zoom level,
that's why I was wondering how it works. And I have a case where there
is only one read in the window, but the numbers in brackets say
[0-361]. Maybe I've set some parameters in a wrong way in the
alignment preference window. I will look at that carefully.

Olivia

On 17 avr, 17:00, Jacob Silterra <ja...@broadinstitute.org> wrote:
> Hi Olivia,
>

> Details on the coverage track are available athttps://www.broadinstitute.org/software/igv/AlignmentData.

[Jim Robinson]

Hi Olivia,

Are you referring to the numbers in the upper left corner?  That is the range of the "Y" scale for the bar chart.  So in your example it goes from zero to 361 counts.   

--Jim

[Olivia]

Hi Jim,

it was so simple... Thank you very much, I had just not thought at the
"Y" scale.

Olivia