Families with multiple markers

[shriram patel]

Hi ShortBred folks, 

First of all, I would like to appreciate the time you have provided for making detailed tutorial as well timely answers to users query.

I have observed that, few of the families with multiple markers were excluded (in result file) despite of their valid alignments and high count. Suppose for Family X, out of their 5 True markers, only 3 got the valid hits. So, based on the explanation provided in the tutorial, this family won't be counted because all the markers are not covered or annotated.

But reverse scenario is that families with only single markers will count towards result despite of there lower hit counts than Family X and topped the table. 

And in my all results, I have observed that couple of families with multiple markers and high hits were excluded because all markers were not observed. And one of them is having 9 true markers.

So, is there any criterion or parameter that this much fraction of markers of families should be detected to be counted in results?

Correct me if my understanding is wrong.

Thanks

Shriram

[Eric Franzosa]

Hi Shriram,

The algorithm focuses on the median coverage of each family's markers. Hence, if there is only one marker, we focus on its abundance. If there are multiple (usually smaller) markers, then we focus on their median coverage. If 3 out of 5 were non-zero, that would thus give a non-zero abundance for the whole family. Hope this helps!

Thanks,

Eric

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