> 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/microarray/general/microarray-general-faq-list/000009184.md).

# How does the iScan rescan feature work?

The option to rescan a BeadChip appears after the current scan is complete if any stripes fail registration. Failed stripes are visible as red stripes in the BeadChip graphic. Selecting the Rescan button initiates a rescan of only the sections of the BeadChip that failed registration.

The impact of rescanning varies depending on the file type. The following sections describe how each file type is affected by the rescan process:

1. **IDATs**: For sections being rescanned, the original IDAT (intensity data file) is overwritten, and is not saved.
2. **JPEGs:** For the jpeg images (focus scans and BeadChip stripe images), for the affected sections only, the previous jpegs are re-named, adding the extension "\_old0" to the end of the filename.\
   For example, upon rescan, the stripe image filename "207221130001\_R21C01\_1-Swath1\_Grn.jpg" gets renamed to "207221130001\_R21C01\_1-Swath1\_Grn\_old0.jpg" The scanner then creates a new version of "207221130001\_R21C01\_1-Swath1\_Grn.jpg" based on the rescan of the stripe. Subsequent rescans add "\_old1", "\_old2" and so on, and rewrite a new file with the original filename.
3. **Metrics:** When a rescan is initiated, the original metrics.txt file is renamed in the same way, with "\_old0" appended to the end of the filename, and a new metrics.txt file is created, reflecting the data for the rescan. Only scan data for the rescanned sections are included in the newly updated metrics.txt file. Subsequent rescans add sequentially to the suffix, similar to the jpeg filenames.

**Note**: The Rescan option only appears immediately after the scan of a BeadChip containing sections that failed registration. If the user initiates another regular scan, the Rescan option disappears.

If a BeadChip that has previously been scanned is scanned again during a subsequent regular scan (not a Rescan), the entire original scan folder is overwritten, and any data from the previous scan of the BeadChip is lost.

To preserve the original scan data for comparison with the new scan, use one of the following methods before rescanning the BeadChip:

* Move the original scan folder to a location outside the designated output location before scanning the BeadChip again.
* Designate a different output location before initiating the new scan.

**Reference:**

[iScan System Product Documentation](https://support.illumina.com/downloads/iscan-system-product-documentation.html)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9184), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009184%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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