Hi all,
I am using gsnap to map paired end reads to reference, and got sam file as output. However, it seems that in the file, there are some pairs with only one end mapped to the reference, the other is not. In this case, should I treat this pair as mapped, or not? Since for paired end reads, we consider pair together, what is the meaning of using pairs with one end mapped, the other not?
Any comments would be appreciated.
I am using gsnap to map paired end reads to reference, and got sam file as output. However, it seems that in the file, there are some pairs with only one end mapped to the reference, the other is not. In this case, should I treat this pair as mapped, or not? Since for paired end reads, we consider pair together, what is the meaning of using pairs with one end mapped, the other not?
Any comments would be appreciated.
Comment