> 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/software/general/software-general-reference_material-list/000005078.md).

# Which orientation are the indexes in Top\_Unknown\_Barcodes output from BclConvert?

In general for Illumina sequencers, the index sequences reported in the BCL Convert output file Top\_Unknown\_Barcodes are in the same orientation as they are sequenced/read by the sequencer.

* See [Guidelines for reverse complementing i5 sequences for demultiplexing](/software/general/software-general-reference_material-list/000001800.md) for more information.

There are exceptions depending on the Illumina sequencer, described below.

**NextSeq 1000/2000 and NovaSeq X/X Plus**

For The NextSeq 1000/2000 and NovaSeq X/X Plus platforms, the RunInfo.xml file includes the IsReverseComplement flag. With this flag, the index sequences that BCL Convert recognizes and outputs are in the following orientations in the Top\_Unknown\_Barcodes output file.

* Index 1: the i7 index column is in the forward orientation, matching the orientation if the i7 indexes in the sample sheet.
* Index 2: the i5 index column is in the reverse complement orientation, relative to the sample sheet used for BCL Convert analysis.

**MiSeq i100**

The MiSeq i100 has two scenarios which will affect the reported i5 orientation in the Top\_Unknown\_Barcodes report file.

* Read First Workflow
  * Index 1: the i7 index column is in the forward orientation, matching the orientation if the i7 indexes in the sample sheet.
  * Index 2: the i5 index column is in the reverse complement orientation, relative to the sample sheet used for BCL Convert analysis.
* Index First Workflow
  * Index 1: the i7 index column is in the forward orientation, matching the orientation if the i7 indexes in the sample sheet.
  * Index 2: the i5 index column is in the forward orientation, matching the orientation if the i5 indexes in the sample sheet.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #5078), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001800%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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