Re: [Gmod-ajax] ColorBySize settings

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

Also note: I described changing a config parameter. If you are not an admin
of the jbrowse instance you might have to ask your admin to do this

-Colin

On Tue, Aug 11, 2020 at 11:40 AM Colin <col...@gm...> wrote:

> 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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>