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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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C# Percentage > Q30 by cycle graph #344

Closed IIID-Don closed 1 month ago

IIID-Don commented 2 months ago

Where can I find the data to produce the Percentage greater than Q30 graph as produced on the overview tab of the SAV.

Do I need to calculate it from the imaging table data?

Thanks

Don

ezralanglois commented 2 months ago

See https://github.com/Illumina/interop/issues/198

IIID-Don commented 2 months ago

Thanks ezralanglois,

I managed to get there, but have two questions: 1) What is the C# equivalent of the python command: interop_run.MetricCount 2) When I plot the graph, the SAV Average percent >= Q30 plot on the Overview tab, appears to be the same data as the maximum percent >= Q30, that I got from the interop, should that be the case?

Don

ezralanglois commented 2 months ago

Hi Don,

  1. metric_group.MetricCount
  2. I don't know what you mean by maximum percent >= Q30, so I cannot comment on that.

The per cycle code should always plot %>=Q30 as a candle stick (similar to a box plot).

IIID-Don commented 2 months ago

Thanks Robert,

I originally plotted it as a candlestick, but it was too busy. Also on the Illumina SAV it is not plotted as a candlestick, presumably for the same reason (see image attached). I decided to use candle_stick_point.p50() which appears to be the same as candle_stick_point.y(), but my chart/graph did not match that on the SAV. By hovering over the points on the SAV to see their values, I deduced that the SAV is plotting candle_stick_point.max_value(). I would have thought that either the mean / average (which I can't find in candle_stick_point) or the median (y or p50) would have been better to plot than the maximum (max_value). Do you know why the max_value was chosen in the SAV for this plot? Or have I misunderstood?

Thanks

Don

Screenshot 2024-05-14 at 09 04 40
ezralanglois commented 1 month ago

You would have to reach out to Illumina support. I don't work on SAV and cannot comment on the choices they made.

IIID-Don commented 1 month ago

Thanks Robert,

I have decided that plotting the median is best for my purposes.

I appreciate the help you have given me for using the interop. I'm able to achieve what I set out to do, thanks to this project and your assistance.

All the best

Don