RNAseq: PE50 vs. SR50


For those of you that have done RNAseq (my interest is whole transcriptome - drug vs. control N2 population), I am trying to decide whether SR50 will be good enough or whether I should opt for the more expensive and thorough PE50 option. Very few papers actually report this level of detail. Which would you opt for?

I love paired end sequencing, it’s amazing for de novo assembly, and I suppose there’s a slim chance it would be useful to you if you’re concerned about transcript isoforms - but if all you want is to count reads mapped to an established genome sequence I can’t see why it would be necessary, or even helpful.

Thank you. Makes sense. One follow-up - I am told that it’s okay to do duplicate rather than triplicate of each sample. Again, this isn’t something that’s commonly reported. For the type of study that I plan, is doing samples in duplicate common/acceptable?