Question on the use of paired end reads

[carden24]

You mention in the documentation that when paired end reads are available only one set of the pair should be use. Could you expand the reason for this? Running it with both pairs will generate a wrong results or it will decrease performance,
thanks

Erick

[lmrodriguezr]

The problem with paired reads is that they are not independent events. If your average insert size is longer than twice the read length, the coverage will likely be underestimated. On the other hand, if you have small average insert sizes (close to a read length), the coverage will likely be overestimated. However, if you have a small insert size and you can combine most pairs (e.g., using PEAR), the resulting merged reads are probably better estimators. In all other cases, I recommend simply using one of the sister reads.