Dear Manual,
I got stuck with some basic question regarding your vast-pipeline:
1)
I defined an AS event to pass the minimum coverage in at least 90% of samples in each
condition separately.
I am planing to do Diff part myself based on your last nature paper.
I have some events that they did not pass the minimum coverage threshold
in the healthy control (N,N,N: in the Q column) but those events are SOK in the
patients. Should I include thos events in Diff part?
Or only events which pass the minimum read coverage are valuable as an AS event in Diff?
2)
What does an "N" for any event mean?
So does it reflect a biological property (the event not being there in the sample)?
Or is it an artifact of the underlying experiment (no reads for any reason in
the raw sequence, lab condition,...) and we cannot tell about it
at all (could be there, could not be there)?
Dear Manual, I got stuck with some basic question regarding your vast-pipeline:
1) I defined an AS event to pass the minimum coverage in at least 90% of samples in each condition separately. I am planing to do Diff part myself based on your last nature paper. I have some events that they did not pass the minimum coverage threshold in the healthy control (N,N,N: in the Q column) but those events are SOK in the patients. Should I include thos events in Diff part? Or only events which pass the minimum read coverage are valuable as an AS event in Diff?
2) What does an "N" for any event mean? So does it reflect a biological property (the event not being there in the sample)? Or is it an artifact of the underlying experiment (no reads for any reason in the raw sequence, lab condition,...) and we cannot tell about it at all (could be there, could not be there)?
Kind regards, Rahel