# 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 in Illumina Protein Prep 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 Illumina Protein Prep Automation System output file(s):

1. Find the `Lanes` column in the Illumina Protein Prep 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 Illumina Protein Prep 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 plate (with its controls) and can include 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 Illumina Protein Prep 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 Illumina Protein Prep Automation System output file.
2. Edit `Project` column in an Illumina Protein Prep Automation System output file by assigning a project name to each sample. Project name string should contain only alphanumeric characters and underscores.
3. Upload modified Illumina Protein Prep Automation System output file to the Run Planner.

<mark style="color:orange;">**Note**</mark>: 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.

<mark style="color:orange;">**Note**</mark>: If project splitting is enabled, all samples on one plate must be included in the same project. Samples from one plate CANNOT be split across projects.

## Lane Splitting and Multi-Analysis Examples

Here is an example of what the first lines of two individual IPPAS 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".

<figure><img src="/files/iJmwwfITkBW8zKWBRKPr" alt=""><figcaption></figcaption></figure>

<figure><img src="/files/zy52DVuyfPOF3oZobjjf" alt=""><figcaption></figcaption></figure>


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