Upper limit for flexiplex_filter

[nadiadavidson]

@olliecheng First instance of the filter selecting the wrong rank. See figures below. First in default setting, second is shifting the upper limit to 12000.

[nadiadavidson]

It switched the order of the images on upload, so first image with this custom upper limit and second the default.

[olliecheng]

At the moment the default lower bound is the 0.95 quantile (code). Admittedly I just eyeballed this value because it looks 'about right' with my sample datasets, but it seems to be a bit too strict at times.

A couple of alternative ideas

• BLAZE uses the value of the 0.95 quantile, divided by 20
• BLAZE also includes a 'high sensitivity' setting which uses c0.95 divided by 200. Might be good to include such a flag for those stubborn datasets as an easy fix
• A possibly more reliable approach could look for this region, which tends to correlate to bad reads which should be discarded. These are indicated by regions with hundreds/thousands of reads which all have the same, low count (usually something like <1).
  

What do you think?