I am working on data (RNA-Seq) that was sequenced as 151 bp PE using NovaSeq.
Looking at the QC that was generated after library construction (the library was constructed using TruSeq RNA Access ), the size of the fragments is given as ~300 on average. Since this is after library construction, I understand that this includes adapters as well.
I'm still new in bioinformatics, but I completely fail to understand the logic behind sequencing 151 bp paired end with a fragment that after adapter removal should be around 170 bp only. As far as I understand, R2 would mostly overlap with R1. While 151 bp single read sequencing could make sense, I fail to see the logic behind paired-end sequencing of such a fragment.
The answer I have received from the company as to why 150 paired ending was performed is
"From what we checked, 150PE sequencing is agreed on the quotation and we followed the settings. As the fragments size is longer than 150bp, 150PE sequencing seems acceptable. Additionally the sequencing result shows high quality(e.g. Q30 is higher than 90). If you want it to be 100PE sequencing, please let me know. We will trim the data and send it back to you."
1) Am I correct that sequencing paired-end (as opposed to single-read) was completely useless in this case?
2) Does the person to whom the data belongs have a moral case for asking a refund? While he might not have a legal case (as the company states, 150 PE is agreed on the quotation), I think they should have definitely warned him that 150 paired end is not needed if the biological fragment is 170 bp long. He could have saved part of the money (I guess that a large part, though I don't know) by sequencing single end.