> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/library-preparation/rna-library-prep/library-preparation-rna-library-prep-faq-list/000001399.md).

# Sequencing TruSeq Small RNA libraries

**Should TruSeq Small RNA libraries be sequenced as single-read or paired-end?**\
Illumina recommends sequencing TruSeq Small RNA libraries single read (with a single index read). Paired-end sequencing offers no advantage with TruSeq Small RNA libraries, as the full inserts are sequenced in a single-read run.

**How many cycles of sequencing do small RNA libraries need?**\
Generally, this library type is sequenced single-read, 50 bp (1x50 bp), though this can be adjusted depending on the aim of the experiment.

**Why are there reads that end in adapter sequences?**\
The inserts in these libraries are the small RNA molecules, and are often shorter than the length of the read. Reads longer than the small RNA molecules will sequence into the adapter. Data must be adapter trimmed to remove adapter content. See [Sequences to use for adapter trimming](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000001314?utm_source=agent\&utm_medium=email\&utm_campaign=kb) for additional information.\
\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                              |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #1399), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001399%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://knowledge.illumina.com/library-preparation/rna-library-prep/library-preparation-rna-library-prep-faq-list/000001399.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.