PE/ SE RNA seq

Question

[rob.costa1234]

I approached few cores and they say they do SE on illumina next-seq for RNA-seq and PE is not possible. I was wondering if illumina technology has changed changed recently. I could not find any information while I google that issue. Any pointer will be helpful. I called Illumina and the say one shoudl be able to do PE which add to confusion.

Answer 1

[igor]

Both PE and SE are possible with the same libraries. I have never heard of a core refusing to do something as basic as PE RNA-seq. Most people do SE because it's cheaper (half the sequencing cycles) and the results are not much worse. If they say PE is not possible, it's because they only do very specific workflows and that would interfere with that. Some cores are reluctant to do any customization. Another issue is that the sequencing kits are made for a certain number of cycles. Depending on the number of cycles required, there may not be a kit in that size. For example, if they only have 75-cycle kits, they cannot do a 2x50 run.

For reference, the official Illumina recommendation for TruSeq RNA kit on a NextSeq system is 2x75: http://www.illumina.com/library-prep-array-kit-selector.html