> For the complete documentation index, see [llms.txt](https://help.multiomics.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.multiomics.illumina.com/dragen-protein-quantification/run-setup/lane-splitting-and-project-splitting.md).
# Lane Splitting and Multi-Analysis by Project
## Lane Splitting
The purpose of lane splitting is to enable the reuse of sample indexes (barcodes) on the same flow cell. To accomplish this, the samples indexed with the same barcodes must be physically separated by placing them on different lanes of the flow cell.
Currently, lane splitting functionality with SomaSeq Discovery is only supported on the NovaSeqX platform. To use lane splitting, use the sample sheet to indicate which lane(s) each sample is found in.\
Recommendation: Edit the "Lanes" column of the SomaSeq Automation System output file(s):
1. Find the `Lanes` column in the SomaSeq Automation System output file.
2. Add lane numbers in which the sample is located as a comma-separated value.\
**Example:** '1,2,3,4' for a sample located in lanes 1, 2, 3, and 4.
3. Upload the modified SomaSeq Automation System output file to the [BSSH Run Planner](/dragen-protein-quantification/run-setup/page.md).
## Multi-Analysis by Project
The goal of multi-analysis by project is to improve flexibility by enabling multiple analysis outputs from a single sequencing run without needing to requeue the sample sheet. A single project must include at least one sample and can span multiple plates used in a sequencing run. Each project produces one set of output files (including normalized ADATs and a DRAGEN Report).
To use multi-analysis by project, include the project name in the `Project` column of the SomaSeq Automation System output files. If no project information is provided, DRAGEN Protein Quantification will assume all plates belong to the same project and will assign the project name based on the user provided 'run name'. The multi-analysis by project feature is available for both the NovaSeq 6000 and NovaSeq X platforms.
1. Find the `Project` column in the SomaSeq Automation System output file.
2. Edit `Project` column in an SomaSeq Automation System output file by assigning a project name to each sample. Project name string should contain only alphanumeric characters and underscores. Not all samples on a plate need to belong to the same project—different project values are permitted across samples within a single plate.
3. If multiple projects are used on a single plate, leave the `Project` field blank for control samples (Blanks, Calibrators, QCs). Controls with a blank project value will be shared across all projects on that plate for that KitType.
4. Upload modified SomaSeq Automation System output file to the Run Planner.
There must be a minimum of 1 sample per project.
### Multiple Kit Types on a Single Flowcell
A single flowcell (sequencing run) can contain plates of different kit types (e.g., one Plasma plate and one MultiMatrix plate). Each plate must contain a single kit type with its own controls. During autolaunch, the software performs kit-specific normalization on each plate independently.
If a project includes plates with different kit types or if there are no projects defined and there are multiple kit types on the same flowcell, the software will automatically separate them into separate projects so that each project contains plates of the same kit type. A dataset with two plates of different kit types will produce the same results whether splitting by project or not, as long as each plate is its own kit type.
**NOTE**: If you want all samples from a sequencing run to be analyzed together, DO NOT include any values in the "Project" column of the sample sheet.
### Lane Splitting and Multi-Analysis Examples
Here is an example of what the first lines of two individual SomaSeq Automation System output files may look like after project and lanes values were added. The plate with Barcode "A" adds lanes "1,2,3,4" and project value "ProjectA". The plate with barcode "B" adds lanes "5,6,7,8" and project value "ProjectB".
---
# 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://help.multiomics.illumina.com/dragen-protein-quantification/run-setup/lane-splitting-and-project-splitting.md?ask=&goal=
```
`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.
%20(1)%20(1).png?alt=media)
%20(1).png?alt=media)