> For the complete documentation index, see [llms.txt](https://clipforum.flow.bio/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://clipforum.flow.bio/computational/demultiplexing.md).

# Demultiplexing

**Are the indices in line with read 1? They are also shorter than what our sequencing facility normally uses, are they hard to demultiplex?**

We developed a tool for demultiplexing libraries with complex barcoding (including in-line barcodes), as is the case of iCLIP. The tool is called Ultraplex, it's fast and easy to use, please find here: <https://wellcomeopenresearch.org/articles/6-141>. See Fig1 for an example read from a typical iCLIP library, and the demultiplexing workflow. This tool is also implemented within <https://imaps.goodwright.com/>, a free platform for password-protected data analysis dedicated especially to CLIP.


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