RNA-seq stranded protocol

Question

[runningonempty]

I understand the differences between stranded and unstranded RNA-seq libraries and the advantages os stranded over unstranded. However, I do not get the advantages of a first vs second-stranded RNA library.

Are these just different experimental protocols that yield the complementary read sequence from each other (when comparing first- vs second-strand libraries) or is there something else?

I do not get why some RNA-seq experiments are generated following first-strand and other employin second-strand libraries approaches.

Thanks for your help!

Answer 1

[Istvan Albert]

Here is a paper that goes into more detail about the pros and cons

Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data, Briefings in Functional Genomics, 2020

https://academic.oup.com/bfg/article/19/5-6/339/5837822

For first strand synthesis, strand information is preserved by degrading the non-template strand and PCR amplifying only the template cDNA strand during library construction Second strand protocols preserve strand information by using adapters to mark the template strand.