I had this question too and I just checked their adapters and primers to figure out the answer. My conclusion is that their design is correct:
For ChIP-exo, you typically perform single-end sequencing, not paired-end sequencing. The Illumina R1 sequencing primer anneals to the P5 site, which does contain the extra T that is normally used for A-overhang ligation. The P7 site indeed misses a T compared to regular libraries, but this is not an issue as long as you don't intend to perform PE sequencing.
I just wonder why they decided to perform blunt-end ligations... I would expect ligations with an A-overhang to be more efficient. Does anyone have any experience with this?
For ChIP-exo, you typically perform single-end sequencing, not paired-end sequencing. The Illumina R1 sequencing primer anneals to the P5 site, which does contain the extra T that is normally used for A-overhang ligation. The P7 site indeed misses a T compared to regular libraries, but this is not an issue as long as you don't intend to perform PE sequencing.
I just wonder why they decided to perform blunt-end ligations... I would expect ligations with an A-overhang to be more efficient. Does anyone have any experience with this?
Comment