huge duplicates or high expression

[yuliu]

Hi,

In my analysis, I found more than 10,000 paired-end reads aligned in same region. all of 10,000 reads start from same position, and its pair end at another same position. How can I distinguish it is duplicate or true expression? Any idea will be appreciated.

best
Yu

[SNPsaurus]

It it was high expression, you would expect many reads that start and stop at different parts of the transcript. Since your paired-end reads indicate the same DNA fragment was sequenced each time, duplication is what is happening.