Dear Forum Members,
First my apologies if this is not the correct forum thread for my question.
Im working on RNA-seq PE.
Lets say one was looking at events that are rare (low coverage), what is the general consensus (considerations) regarding the validity of such data.
I have looked through litterature and this is not always taken into consideration I believe.
E.g. if < 5 read pairs support an observation.
Having >300.000.000 from a single flow lane, then just by chance one could expect a read pair to be false e.g. wrong mates are connected or something else strange thing happening. I guess this comes down to the accuracy of NGS, validation by conventional techniques (if possible), sequence identity to the specific region etc.
However, what is your opinion in this respect?
First my apologies if this is not the correct forum thread for my question.
Im working on RNA-seq PE.
Lets say one was looking at events that are rare (low coverage), what is the general consensus (considerations) regarding the validity of such data.
I have looked through litterature and this is not always taken into consideration I believe.
E.g. if < 5 read pairs support an observation.
Having >300.000.000 from a single flow lane, then just by chance one could expect a read pair to be false e.g. wrong mates are connected or something else strange thing happening. I guess this comes down to the accuracy of NGS, validation by conventional techniques (if possible), sequence identity to the specific region etc.
However, what is your opinion in this respect?