single end 50bp or paired end 2x100

[xiaohuituzhi]

Hi everyone,

I am planning to do RNA-Seq on RNA extracted from breast cancer cells, the main purpose is to identify differentially expressed genes after stimulation. Now I got two quotations from two companies.

Company A: single end 50bp, 10M clean reads per sample

Company B: paired end 2x100bp, 10M reads per sample

The price from company B is 25% lower than company A. This is quite confusing, isn't PE and longer reads more expensive?

Can anyone give me some suggestions? That will help me a lot because I am really new to the sequencing technology..Thanks a lot!

Best,
Frank

[nucacidhunter]

Generally 2x100 is more expensive than 50 SR. There seem to be a difference between two offers. Offer A states clean read and you need to get clarification what that means by them. For instance, it may mean quality filtered, mappable reads free from adapter dimers or reads from shorter than 50 bp inserts. You can always trim down 2x100 reads if you want. I think that 10M reads perhaps is in lower side for differential expression analysis.