[BioC] duplicate reads in mRNA-Seq

[Jason Lu]

Hi,

Some of you may have answers for this.

It seems that the duplicate reads are very common in mRNA-seq data.
Duplicate reads are those being mapped to exact the same chromosome
location and on the same strand (maybe from PCR amplification). I
would like to know what are the general practice to deal with it? I
suspect some of those may contribute to the large overdispersion in
the final count data.

Thanks,

Jason