> For the complete documentation index, see [llms.txt](https://nks.gitbook.io/rna-seq/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://nks.gitbook.io/rna-seq/3.-good-to-know-beforehand/single-end-and-paired-end.md).

# Single-end and Paired-end

It basically means do you want each fragment to be sequenced from only one direction or both directions (3' and 5').  The purpose is to increase the specificity for genes assemble that are significantly longer than the read length, [among others](https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html).