Re: [Gmod-ajax] ColorBySize settings

[Colin <col...@gm...>]

Hi Caterina,

Glad to hear about interest in paired end read viewing, it is not a feature
that we've received a lot of feedback about since it was launched. There
are not a lot of manual tuning parameters currently, but I try will
describe the algorithm it uses.

- First, if there are too few features, e.g. less than 100
(config.insertStatsCacheMin) then it exits because the statistics might not
be good

- Next, it calculates mean and variance of insert size for all reads in
view except for read pairs that have insert size below a configurable
minimum (config.insertStatsMinSize) and maximum (config.insertStatsMaxSize)

- Then it colors things if they are below or above mean+/-3*sd

The default minimum is 100 (config.insertStatsMinSize), the maximum is
50,000 (config.insertStatsMaxSize)

If you think maybe reads with long insert size (e.g. in the range
450-50,000) are affecting the calculation, you could try changing
"insertStatsMaxSize": 500 so this way it will actually only take into
account reads below insert size 500 for the stats calculation, and then it
will more clearly show anything above this range


Let me know if that helps

-Colin

On Tue, Aug 11, 2020 at 9:56 AM Caterina Marconi <cat...@ho...>
wrote:

> Hello,
> I have two question regarding the ColorBySize option.
> What is the correct way to use the "re-estimate insert size stats"
> function?
> Is it possible to set a fix thresholds for insert size for the
> ColorBySize option?
> I have some troubles in visualizing abnormal read-pairs. The avg insert
> size is around 450bp, but only reads with insert size higher than 1000 are
> highlighted. Moreover, if I switch from paired to unpaired view and then
> again to pair view, I lost the highlighting.
>
> Thanks for your help.
> Caterina
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