NanoCount MIN_QUERY_FRACTION_ALIGNED parameter default setting

[kir1to455]

Hi, @josiegleeson
Thank you for developing NanoCount .
I would like to know why MIN_QUERY_FRACTION_ALIGNED default setting is 0.5 ?
The reason why I asked this question is that I encountered a situation that puzzled me.

I have a 7268 bp read with 6238S(soft clip). By default, this read will be filtered out by NanoCount becaues the QUERY_FRACTION_ALIGNED nearly to 14%.
Do you think this read should be retained?

Best wishes,
Kirito

[josiegleeson]

Hi Kirito,

Hmm I think that because only a small fraction of the read is actually aligning, its at least a red flag that something strange is going on. You could trying taking the unaligned 6k bp section and seeing what it is.

But I think in majority of the cases I've seen I'd lean towards not using this read..

Let me know what you think,
Josie