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.