Hi all,

After mapping, I used IGV to have a look at the mapping. There are a lot of mapped reads without pair reads. Should I keep these reads? or Is this a problem for cufflinks analysis?

What I tried is:
1. BAM to SAM
2. Filter SAM:  set Read mapped in a proper pair to Yes.
The result is that only 1/5 reads were left.

Can anybody tell me if this operation is proper??
How do you normally optimize the mapping rerults from Tophat?
Which considerations should I take into account?
Looking forward to your reply.
Jiwen