Y axis on IGV coverage track

[David]

I am comparing densities of NGS reads from two timepoints using IGV. The coverage track gives a nice topography of reads, but no Y axis units. Is there a way to visualise what these units are please? Thanks, David.

[Jim Robinson]

Yes, in the user preferences (View > Preferences) select the
"Charts" panel and there is an option to label the y axis.

Jim

[David]

I have done this but no Y axis appears. There is a number at the top of the coverage track [0-97] and I can see the total counts by moving the mouse over the peaks. Do you have any idea what I might be missing to get a Y axis - where exactly on the page should it appear? Thanks, David.

[Jim Robinson]

Hi,

I just discovered it doesn't appear in the "whole genome" view, this is
a bug. However, if you go to a chromosome it should appear on the left
hand side as shown in the attached screenshot.

Jim

[David]

Thanks -this would be exactly what I need. I am looking at a specific chromosome region and I don't see it. the exact bit is chr4:116,281,886-116,284,907, and I am visualising NGS as a bam file. Should I be able to see the scale bar? Many thanks, David.

[David]

Jim, One other question. Are the numbers in the Y axis that you show the actual read number range, from 0-4817 in the top track? Thanks

[Jim Robinson]

David, apologies but this option doesn't appear to be operable for
the coverage track, as you noted. I wasn't aware of that, we'll fix it.

The number at the top is the range displayed, you really don't get more
information by displaying the y-axis as there isn't room for tick
marks. You can right click on the track and explicitly set a range,
by default it auto-scales.

Jim

[David]

Many thanks. One last question -when you say range is that the range of individual read numbers? Thanks, David.

[Jim Robinson]

That is the Y data range for the bar chart, so the numbers are read
count.

[Rashmi Jain]

hi

I am also working of IGV to visualize TDF file. Y-axis value is coming in decimal. Is this average number of reads. it is 0-413.57.

Thank you

Rashmi

[Jim Robinson]

You specify a window size when computing coverage,  by default its 25 bp,  this is the average over that window.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/345c007c-1020-453f-91f5-e47b6c3fc5a6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.