single- indexed sequenced as paired end

Question

[amitpande74]

Hi,

I recently got some chip-seq data to analyze. I noticed that 60% of the reads did not align to the human genome. After little bit of investigation I came to know that single indexed samples were sequenced as paired end. So, I wrote a very humble e-mail to the company which sequenced the samples. The reply that I received is as follows:

 Please don’t worry, even your library is single- indexed, it is OK to sequence as pair end reads. There are single index and dual index difference in pair end reads

Am I the only one who does not understand this? Kindly help.

Answer 1

[GenoMax]

There is no correlation between single or dual indexing (and single-end or paired-end reads for that matter) and the reads not aligning to expected reference. You will need to investigate what is in those 60% reads and then follow-up with the sequence provider, if you can prove that there is unexpected contamination in your data. This conversation is always tricky. Provider can claim that your samples originally contained the contamination. So be ready to work through these issues.