> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-transcriptome-cufflinks.md).
# Quantify to transcriptome (Cufflinks)
Cufflinks assembles transcripts and estimates transcript abundances on aligned reads. Implementation details are explained in Trapnell et al. \[1]
The Cufflinks task has three options that can be configured (Figure 1):
* **Novel transcript**: this option does not require any annotation reference, it will do de novo assembly to reconstruct transcripts and estimate their abundance
* **Annotation transcript**: this option requires an annotation model to quantify the aligned reads to known transcripts based on the annotation file.
* **Novel transcript with annotation as guide**: this option requires an annotation file to quantify the aligned reads to known transcripts as well as assemble aligned reads to novel transcripts. The results include all transcripts in the annotation file plus any novel transcripts that are assembled.
When the Use bias correction check box is selected, it will use the genome sequence information to look for overrepresented sequences and improve the accuracy of transcript abundance estimates.
## References
1. Trapnell C, Williams B, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotech. 2010; 28:511-515.
## Additional Assistance
If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.
---
# 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 by asking a question.
Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:
```
GET https://help.bioinsight.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-transcriptome-cufflinks.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.
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.
%20(1)%20(1)%20(1)%20(1)%20(1)%20(1)%20(1)%20(1)%20(1)%20(1)%20(1).png?alt=media)